Thank you Bruce,
Please guide me how can I use mri_surf2vol command on lh/rh.thickness files to get the output as lh/rh.ribbon.nii for AFNI SUMA. Thank you
Best Regards,
Muhammad Naveed Iqbal Qureshi
From: freesurfer-request@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 119, Issue 6 To: freesurfer@nmr.mgh.harvard.edu Date: Mon, 6 Jan 2014 10:51:33 -0500
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Today's Topics:
- erroneuos segmentation labeling of skull outside of brain (Yuliya Yoncheva)
- Re: erroneuos segmentation labeling of skull outside of brain (Bruce Fischl)
- Re: Motion correction for SPACE FLAIR (Bruce Fischl)
- Re: erroneuos segmentation labeling of skull outside of brain (Yuliya Yoncheva)
- Re: erroneuos segmentation labeling of skull outside of brain (Bruce Fischl)
- Re: recon-all exited w/errors (Bruce Fischl)
- ROI masks created in FreeSurfer used in FSL?? (Frank Hsieh)
- converting .thickness files of T1 MRI from FreeSurfer into AFNI (Muhammad Naveed Iqbal Qureshi)
- brain orientation in qdec (L. Schweren)
- Re: converting .thickness files of T1 MRI from FreeSurfer into AFNI (Bruce Fischl)
- recon-all error (Emad Ahmadi)
- Fwd: Anatomical segmentation - question (Rotem Saar)
Message: 1 Date: Sun, 5 Jan 2014 15:14:39 -0500 From: Yuliya Yoncheva yuliya.yoncheva@gmail.com Subject: [Freesurfer] erroneuos segmentation labeling of skull outside of brain To: freesurfer@nmr.mgh.harvard.edu Message-ID: CAGE5uFc2uD9pMefXjRZE0LQP+GcfhHKWeVkHxOGwDzV1=jYrQA@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"
Dear FreeSurfer community,
I am visually inspecting the quality of my recon -all output for a large dataset and have a rookie question.
In some instances, when skull stripping ended up leaving some of the skull, these voxels are associated with a "sgmtn label" (cerebral cortex). In other instances, although there are a small number of skull voxels that were not removed automatically, these voxels do not have an associated "sgmnt label" available in TkMedit Tools.
Is it the case that only the voxels for which there is a segmentation label are actually added to the total grey volume estimate?
Thus, voxels, which have not been automatically labelled would not impact volume computations?
Thank you kindly for your help. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140105/39... -------------- next part -------------- A non-text attachment was scrubbed... Name: ExCerCor.png Type: image/png Size: 81100 bytes Desc: not available Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140105/39...
Message: 2 Date: Sun, 5 Jan 2014 15:40:24 -0500 (EST) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] erroneuos segmentation labeling of skull outside of brain To: Yuliya Yoncheva yuliya.yoncheva@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.03.1401051539450.16518@nmr.mgh.harvard.edu Content-Type: text/plain; charset="iso-8859-1"
Hi Yuliya
they are included if they are inside of the ?h.pial surface. We don't use the cortex aseg label as it is in general less accurate than the surfaces.
cheers Bruce On Sun, 5 Jan 2014, Yuliya Yoncheva wrote:
Dear FreeSurfer community, I am visually inspecting the quality of my recon -all output for a large dataset and have a rookie question.
In some instances, when skull stripping ended up leaving some of the skull, these voxels are associated with a "sgmtn label" (cerebral cortex). In other instances, although there are a small number of skull voxels that were not removed automatically, these voxels do not have an associated "sgmnt label" available in TkMedit Tools.
Is it the case that only the voxels for which there is a segmentation label are actually added to the total grey volume estimate??
Thus, voxels, which have not been automatically labelled would not impact volume computations?
Thank you kindly for your help.
Message: 3 Date: Sun, 5 Jan 2014 15:55:13 -0500 (EST) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Motion correction for SPACE FLAIR To: Octavian Lie octavian.lie@gmail.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.03.1401051554470.16518@nmr.mgh.harvard.edu Content-Type: text/plain; charset="windows-1252"
Hi Octavian
it's not so easy to reduce the bandwidth in the T2-space sequences, but certainly you can try. Geometry-matched just means that the FOV and matrix sizes are the same.
cheers Bruce On Fri, 3 Jan 2014, Octavian Lie wrote:
Dear Bruce,
Best wishes for 2014!
I will heed your advice and cc to the list. Indeed, the MGH protocol I obtained from Andre has one acquisition (NSA). Related, I cc this post:
We have been trying adaptations of the T2spaceFLAIR MGH protocol on our Phillips 3T scanners (sequences called VISTA). Incorporation of the T2 space FLAIR has been mostly successful at editing out the dura from the pial surface. The only concern are minute differences occasionally appearing as small indentations (at most times <1-2mm) between the woFLAIR.pial and the final pial surfaces, including in intrasulcal (duraless) areas; the amount of these small mismatches is variable from patient to patients, with some trials with almost perfect overlap, and others with visible, if small, differences. I wonder if this has been your experience too, and if this is due mostly to bb registration limits or to differences in pixel bandwidth between mprage and space flair sequences (in our case, see below). In FSwiki, the recommendation is that T2 space flair ?should be bandwidth, geometry and readout matched to the mprage?.
- Speaking about pixel bandwidth, logistics most likely would not
allow application of a MEMPR sequence on our Phillips. According to Siemens MPRAGE MGH specs, "exceptions indicate that if a multiple echo sequence is not available, one should choose a bandwidth of 195 Hz/pixel for the MPRAGE". In that case/ using the Siemens Trio MPRAGE protocol as if the MEMPR is not available, how one would adjust the bandwidth in T2spaceFLAIR protocol (currently ~650 in the Siemens space flair and MEMPR protocols) to "match" it to the "simple" MPRAGE protocol (decreasing it to 195 ?). Would it be a workaround? (Please comment on the Siemens case, obviously, I do not expect any light on Phillips without further testing). 2. Could you clarify what geometry matched means? Please advise,
Thank you,
Octavian
On Fri, Jan 3, 2014 at 9:12 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Octavian
can you cc the list so that others can answer? What is NSA? We don't have a ton of experience with it, but 1 has seemed ok (not sure if we've ever tried two) Bruce
On Thu, 2 Jan 2014, Octavian Lie wrote:
Dear Bruce,
Thank you. We used one vs 2 NSA T2 space FLAIR sequences, without a consistent difference in results, with the 2-NSA run obviously doubling the scan time. Is there a preferred number of NSA you recommend, or we should be fine with one? Both are at resolution 1X1X1 mm. Thank you,
Octavian
On Thu, Jan 2, 2014 at 11:56 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Octaviaan no, not really. You should motion correct and average them using something like mri_motion_correct*
We do typically bandwidth/readout match them to the memprages so that there is no differential distortion cheers Bruce On Wed, 1 Jan 2014, Octavian Lie wrote: Dear All, We recently implemented pial correction using T2 space FLAIR with freesurfer v 5.3, mostly successfully. We use 2-3 MPRAGE (sagittal + axial and/or coronal) volumes as 001.mgz, 002/003.mgz for the motion correction step in recon-all pipeline. The typical times for acquiring space FLAIR in our settings vary from 2.5 to 6 min, depending on the resolution/NSA no. I was wondering how freesurfer deals with motion artifacts in the space FLAIR sequence (especially with longer acquisition times), and if there is a strategy to minimize motion distortion with these (such as getting second runs for averaging, etc). Please advise, Octavian.The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Message: 4 Date: Sun, 5 Jan 2014 19:25:53 -0500 From: Yuliya Yoncheva yuliya.yoncheva@gmail.com Subject: Re: [Freesurfer] erroneuos segmentation labeling of skull outside of brain To: Bruce Fischl fischl@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: CAGE5uFcchoLxBvaf5Lze9z9_QPU4NGa83WFwZ90auZX3-idsFg@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"
Hello Bruce,
thank you very much for your fast response and clarifying that potential voxels outside the pial surface do not impact cortical measures.
Best, Yuliya
On Sun, Jan 5, 2014 at 3:40 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Yuliya
they are included if they are inside of the ?h.pial surface. We don't use the cortex aseg label as it is in general less accurate than the surfaces.
cheers Bruce
On Sun, 5 Jan 2014, Yuliya Yoncheva wrote:
Dear FreeSurfer community,
I am visually inspecting the quality of my recon -all output for a large dataset and have a rookie question.
In some instances, when skull stripping ended up leaving some of the skull, these voxels are associated with a "sgmtn label" (cerebral cortex). In other instances, although there are a small number of skull voxels that were not removed automatically, these voxels do not have an associated "sgmnt label" available in TkMedit Tools.
Is it the case that only the voxels for which there is a segmentation label are actually added to the total grey volume estimate?
Thus, voxels, which have not been automatically labelled would not impact volume computations?
Thank you kindly for your help.
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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Message: 5 Date: Sun, 5 Jan 2014 20:29:06 -0500 (EST) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] erroneuos segmentation labeling of skull outside of brain To: Yuliya Yoncheva yuliya.yoncheva@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.03.1401052028520.16518@nmr.mgh.harvard.edu Content-Type: text/plain; charset="iso-8859-1"
exactly, or measures derived them them like whole-brain volume
cheers Bruce
On Sun, 5 Jan 2014, Yuliya Yoncheva wrote:
Hello Bruce, thank you very much for your fast response and clarifying that potential voxels outside the pial surface do not impact cortical measures.
Best,? Yuliya
On Sun, Jan 5, 2014 at 3:40 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Yuliya
they are included if they are inside of the ?h.pial surface. We don't use the cortex aseg label as it is in general less accurate than the surfaces. cheers Bruce On Sun, 5 Jan 2014, Yuliya Yoncheva wrote: Dear FreeSurfer community, I am visually inspecting the quality of my recon -all output for a large dataset and have a rookie question. In some instances, when skull stripping ended up leaving some of the skull, these voxels are associated with a "sgmtn label" (cerebral cortex). In other instances, although there are a small number of skull voxels that were not removed automatically, these voxels do not have an associated "sgmnt label" available in TkMedit Tools. Is it the case that only the voxels for which there is a segmentation label are actually added to the total grey volume estimate?? Thus, voxels, which have not been automatically labelled would not impact volume computations? Thank you kindly for your help.The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Message: 6 Date: Sun, 5 Jan 2014 20:50:51 -0500 (EST) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all exited w/errors To: "Boric, Katica A." KBORIC@mgh.harvard.edu Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.03.1401052049480.16518@nmr.mgh.harvard.edu Content-Type: text/plain; charset="iso-8859-1"
Hi Katica
what format was the input image to recon-all? Can you verify that tkmedit has the directions correct (that is what it labels as anterior is actually anatomically anterior, etc...). If so, then the talairach just failed and you will need to either try an alternative (like the MNI or SPM talairachs) or generate it manually.
cheers Bruce
On Thu, 2 Jan 2014, Boric, Katica A. wrote:
Happy New Year freesuerfers! I run into this error while doing?recon-all :
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string.
I would really appreciate if someone could give me some advice on how to fix this error.
Thank you very much!
Katica Boric,
ps:?Here is the error log:
#@# Talairach Failure Detection Thu Jan ?2 14:20:32 EST 2014 /home/XX/XXX/subjects/XXX_SurferOutput/mri
?talairach_afd -T 0.005 -xfm transforms/talairach.xfm?
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) INFO: Attempting MINC mritotal to perform Talairach align #-------------------------------------------- #@# Talairach Thu Jan ?2 14:20:33 EST 2014 /home/XX/XXX/subjects/XXX_SurferOutput/mri
?mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz?
?talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm?
/home/XX/XXX/subjects/XXX_SurferOutput/mri /usr/local/freesurfer/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Thu Jan ?2 14:21:30 EST 2014 tmpdir is transforms/tmp.talairach.34005 /home/XX/XXX/subjects/XXX_SurferOutput/mri mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc? $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=8.23, TE=3.22, TI=450.00, flip angle=12.00 i_ras = (-1, -9.03383e-08, 0) j_ras = (-1.3411e-07, 2.66591e-08, -1) k_ras = (1.59256e-07, 1, -5.93718e-09) writing to transforms/tmp.talairach.34005/src.mnc...
mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.34005/src.mnc transforms/talairach.auto.xfm Legacy library shellwords.pl will be removed from the Perl core distribution in the next major release. Please install it from the CPAN distribution Perl4::CoreLibs. It is being used at /usr/local/freesurfer/mni/bin/mritotal, line 460. ? ? Thu Jan ?2 14:21:43 EST 2014 talairach done
?cp transforms/talairach.auto.xfm transforms/talairach.xfm?
#-------------------------------------------- #@# Talairach Failure Detection Thu Jan ?2 14:21:44 EST 2014 /home/XX/XXX/subjects/XXX_SurferOutput/mri
?talairach_afd -T 0.005 -xfm transforms/talairach.xfm?
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s xxx_SurferOutput exited with ERRORS at Thu Jan ?2 14:21:45 EST 2014
Message: 7 Date: Sun, 5 Jan 2014 23:35:55 -0800 From: Frank Hsieh two.frank@gmail.com Subject: [Freesurfer] ROI masks created in FreeSurfer used in FSL?? To: freesurfer@nmr.mgh.harvard.edu Message-ID: CABBeRCEt37ZwE1-jHuZGC3Vw-D_v2+svOAnQUcSP6kW37qT4oQ@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"
Dear FreeSurfer Users,
I ran recon -all on my structural image and created ROI masks (using mri_label2vol) based on FreeSurfer's cortical parcellation. I'd like to use these masks for further analysis with FSL. However, it seems that the ROI masks generated with mri_label2vol have different header information than that of the original structural image. As a result, I was unable to carry out further analysis with FSL (e.g., converting these ROI masks into functional space with hires2example_func.mat). I was wondering if there is a way to solve this issue.
Many thanks in advance. Frank -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140105/a5...
Message: 8 Date: Mon, 6 Jan 2014 17:11:54 +0900 From: Muhammad Naveed Iqbal Qureshi mniqureshi@hotmail.com Subject: [Freesurfer] converting .thickness files of T1 MRI from FreeSurfer into AFNI To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: BLU174-W27296B6C59F4D34F89293AC4B70@phx.gbl Content-Type: text/plain; charset="ks_c_5601-1987"
Hi, I want to know that how can I convert FreeSurfer .thickness files to AFNI readable format I tried the following Command but it gives error
mri_convert /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik... AFNI BRIK write unsupported ERROR: failure writing /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik UN:/media>
Please let me help me to solve this problem Thank you :)
Best Regards,
Muhammad Naveed Iqbal Qureshi
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Message: 9 Date: Mon, 6 Jan 2014 10:45:52 +0100 From: "L. Schweren" l.j.s.schweren@umcg.nl Subject: [Freesurfer] brain orientation in qdec To: freesurfer@nmr.mgh.harvard.edu Message-ID: 005601cf0ac4$16bda9b0$4438fd10$@umcg.nl Content-Type: text/plain; charset="us-ascii"
Dear experts,
I ran recon-all with qcache. When loading the right hemisphere of fsaverage (or any other surface reconstruction) into tksurfer (for example command: tksurfer fsaverage rh white), the left hemisphere surface is displayed, and it is upside down. When I import annotations they load in the same orientation as the surface. However, the coordinates and the labels, displayed in the Tksurfer Tools window, are not. For example, when I move the cursor to the temporal lobe, the label says it's postcentral. I do not mind manually turning the surfaces in tksurfer, but I do need to be sure I am looking at the correct hemispheres, coordinates and labels.
I hope you can help me solve this. Thank you in advance.
Best wishes,
Lizanne
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Message: 10 Date: Mon, 6 Jan 2014 08:41:58 -0500 (EST) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] converting .thickness files of T1 MRI from FreeSurfer into AFNI To: Muhammad Naveed Iqbal Qureshi mniqureshi@hotmail.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.03.1401060840550.16518@nmr.mgh.harvard.edu Content-Type: text/plain; charset="iso-8859-15"
Hi Muhammad
try:
set sdir=/home/naveed/freesurfer/subjects/CHR01/surf mris_convert -c $sdir/rh.thickness $sdir/rh.orig $sdir/rh.thickness.brik
cheers Bruce
On Mon, 6 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Hi, I want to know that how can I convert FreeSurfer .thickness files to AFNI readable format I tried the following Command but it gives error
mri_convert /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik... AFNI BRIK write unsupported ERROR: failure writing /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik UN:/media>
Please let me help me to solve this problem Thank you :)?
Best Regards, Muhammad Naveed Iqbal Qureshi
Message: 11 Date: Mon, 6 Jan 2014 10:40:43 -0500 (EST) From: "Emad Ahmadi" emad@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all error To: freesurfer@nmr.mgh.harvard.edu Message-ID: 63234.172.19.2.113.1389022843.squirrel@mail.martinos.org Content-Type: text/plain; charset="iso-8859-1"
Hello & Happy New Year!
I'm running recon-all for one subject on MGH clusters (ERISone), and it exits with error. I would appreciate it if you help me figure out what the problem is. The log file is attached.
All the best throughout 2014! Emad
Emad Ahmadi, MD
Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School
25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: emad@nmr.mgh.harvard.edu
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Message: 12 Date: Mon, 6 Jan 2014 17:51:18 +0200 From: Rotem Saar saar.rotem@gmail.com Subject: [Freesurfer] Fwd: Anatomical segmentation - question To: freesurfer@nmr.mgh.harvard.edu Message-ID: CAMjFEmbcEwbXMOyxw-kuep6NSzdnk=rYHSEvwPGSbiXkBZKxtA@mail.gmail.com Content-Type: text/plain; charset="windows-1252"
Dear freesurfer experts,
I'm performing anatomical segmentation for Philips dicoms (3T scanner). I got these two images from the same slice while performing step number 4 in the script below ? from some reason, the two images don't fit. Should I use "scale brain" ? I know this is not recommended thus want to consult with u first ? Can u please comment on why this is happening? Is there any value that corresponds to "how good is the segmentation" ? if yes, where can I find it ?
My script is written below.
Thanks,
Rotem
Anatomical segmentation:
first step- 23 hours:
*recon-all -autorecon-all -i ~/Desktop/ FOLDER-NAME /I00001.dcm -s FOLDER-NAME*
second step:(gyrus=green, sulcus=red)
*tksurfer -curv FOLDER-NAME lh/rh inflated*
third step: (talairch registretion)
*tkmedit FOLDER-NAME brainmask.mgz*
File-> transforms-> load transform AUX-> Browse-> talairch.xfm
forth step: (simetry - allows changing 12df transformation. if we made any changes we should click "save reg" and run this command again)
*tkregister2 --mgz --s FOLDER-NAME --fstal --surf orig*
IF WE CHANGE ANYTHING, CLICK "SAVE REG" AND RUN FROM STARTING POING: recon-all -all -subjectid FOLDER-NAME
fifth step: (scalp removal: if removed too much, rise up from the value 25:
*recon-all -skullstrip -wsthresh 25 -clean-bm -no-wsgcaatlas -s FOLDER-NAME *
to check the result press: *tkmedit FOLDER-NAME brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white *)
for hand correction: *tkmedit FOLDER-NAME brainmask.mgz -aux T1.mgz*
tools-> configure volume brush -> MARK: mode=clone, source=Aux
tools-> configure brush info (for choosing brush size)
click on edit voxels: click in MIDDLE for adding voxels, RIGHT for removing voxels : slice by slice.
when finish, click: File-> save main volume
sisxt step: (cp for correcting segmentation)
*tkmedit FOLDER-NAME brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white*
seventh step: (done)
*recon-all -autorecon2-cp -autorecon3 -s FOLDER-NAME*
Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev Beer-Sheva 84105 Israel -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140106/3d... -------------- next part -------------- A non-text attachment was scrubbed... Name: 3.png Type: image/png Size: 299694 bytes Desc: not available Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140106/3d...
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End of Freesurfer Digest, Vol 119, Issue 6
Hi Muhammad
have you looked at the help? It's pretty extensive. If you have trouble post again and Doug should be able to guide you
cheers Bruce On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Thank you Bruce, Please guide me how can I use mri_surf2vol command on lh/rh.thickness files to get the output as lh/rh.ribbon.nii for AFNI SUMA. Thank you
Best Regards, Muhammad Naveed Iqbal Qureshi
From: freesurfer-request@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 119, Issue 6 To: freesurfer@nmr.mgh.harvard.edu Date: Mon, 6 Jan 2014 10:51:33 -0500
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
- erroneuos segmentation labeling of skull outside of brain
(Yuliya Yoncheva) 2. Re: erroneuos segmentation labeling of skull outside of brain (Bruce Fischl) 3. Re: Motion correction for SPACE FLAIR (Bruce Fischl) 4. Re: erroneuos segmentation labeling of skull outside of brain (Yuliya Yoncheva) 5. Re: erroneuos segmentation labeling of skull outside of brain (Bruce Fischl) 6. Re: recon-all exited w/errors (Bruce Fischl) 7. ROI masks created in FreeSurfer used in FSL?? (Frank Hsieh) 8. converting .thickness files of T1 MRI from FreeSurfer into AFNI (Muhammad Naveed Iqbal Qureshi) 9. brain orientation in qdec (L. Schweren) 10. Re: converting .thickness files of T1 MRI from FreeSurfer into AFNI (Bruce Fischl) 11. recon-all error (Emad Ahmadi) 12. Fwd: Anatomical segmentation - question (Rotem Saar)
Message: 1 Date: Sun, 5 Jan 2014 15:14:39 -0500 From: Yuliya Yoncheva yuliya.yoncheva@gmail.com Subject: [Freesurfer] erroneuos segmentation labeling of skull outside of brain To: freesurfer@nmr.mgh.harvard.edu Message-ID: CAGE5uFc2uD9pMefXjRZE0LQP+GcfhHKWeVkHxOGwDzV1=jYrQA@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"
Dear FreeSurfer community,
I am visually inspecting the quality of my recon -all output for a large dataset and have a rookie question.
In some instances, when skull stripping ended up leaving some of the
skull,
these voxels are associated with a "sgmtn label" (cerebral cortex). In other instances, although there are a small number of skull voxels that were not removed automatically, these voxels do not have an associated "sgmnt label" available in TkMedit Tools.
Is it the case that only the voxels for which there is a segmentation
label
are actually added to the total grey volume estimate?
Thus, voxels, which have not been automatically labelled would not impact volume computations?
Thank you kindly for your help.
Hi Bruce, I have tried to convert by using the following commands but still some error occur.
UN:~> set subj=/home/naveed/freesurfer/subjects/CHR01/ UN:~> mri_surf2vol --surfval surf/rh.thickness --hemi rh --fillribbon --template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii gdiagno = -1 ERROR: cannot recognize the type of surf/rh.thickness
Can you help me. Thank you.
Best Regards,
Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:13:45 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
Hi Muhammad
have you looked at the help? It's pretty extensive. If you have trouble post again and Doug should be able to guide you
cheers Bruce On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Thank you Bruce,
Please guide me how can I use mri_surf2vol command on lh/rh.thickness files to get the output as lh/rh.ribbon.nii for AFNI SUMA. Thank you
Best Regards, Muhammad Naveed Iqbal Qureshi
From: freesurfer-request@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 119, Issue 6 To: freesurfer@nmr.mgh.harvard.edu Date: Mon, 6 Jan 2014 10:51:33 -0500
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
- erroneuos segmentation labeling of skull outside of brain
(Yuliya Yoncheva) 2. Re: erroneuos segmentation labeling of skull outside of brain (Bruce Fischl) 3. Re: Motion correction for SPACE FLAIR (Bruce Fischl) 4. Re: erroneuos segmentation labeling of skull outside of brain (Yuliya Yoncheva) 5. Re: erroneuos segmentation labeling of skull outside of brain (Bruce Fischl) 6. Re: recon-all exited w/errors (Bruce Fischl) 7. ROI masks created in FreeSurfer used in FSL?? (Frank Hsieh) 8. converting .thickness files of T1 MRI from FreeSurfer into AFNI (Muhammad Naveed Iqbal Qureshi) 9. brain orientation in qdec (L. Schweren) 10. Re: converting .thickness files of T1 MRI from FreeSurfer into AFNI (Bruce Fischl) 11. recon-all error (Emad Ahmadi) 12. Fwd: Anatomical segmentation - question (Rotem Saar)
Message: 1 Date: Sun, 5 Jan 2014 15:14:39 -0500 From: Yuliya Yoncheva yuliya.yoncheva@gmail.com Subject: [Freesurfer] erroneuos segmentation labeling of skull outside of brain To: freesurfer@nmr.mgh.harvard.edu Message-ID: CAGE5uFc2uD9pMefXjRZE0LQP+GcfhHKWeVkHxOGwDzV1=jYrQA@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"
Dear FreeSurfer community,
I am visually inspecting the quality of my recon -all output for a large dataset and have a rookie question.
In some instances, when skull stripping ended up leaving some of the
skull,
these voxels are associated with a "sgmtn label" (cerebral cortex). In other instances, although there are a small number of skull voxels that were not removed automatically, these voxels do not have an associated "sgmnt label" available in TkMedit Tools.
Is it the case that only the voxels for which there is a segmentation
label
are actually added to the total grey volume estimate?
Thus, voxels, which have not been automatically labelled would not impact volume computations?
Thank you kindly for your help. -------------- next part -------------- An HTML attachment was scrubbed... URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140105/3
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Message: 2 Date: Sun, 5 Jan 2014 15:40:24 -0500 (EST) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] erroneuos segmentation labeling of skull outside of brain To: Yuliya Yoncheva yuliya.yoncheva@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.03.1401051539450.16518@nmr.mgh.harvard.edu Content-Type: text/plain; charset="iso-8859-1"
Hi Yuliya
they are included if they are inside of the ?h.pial surface. We don't use the cortex aseg label as it is in general less accurate than the surfaces.
cheers Bruce On Sun, 5 Jan 2014, Yuliya Yoncheva wrote:
Dear FreeSurfer community, I am visually inspecting the quality of my recon -all output for a large dataset and have a rookie question.
In some instances, when skull stripping ended up leaving some of the
skull,
these voxels are associated with a "sgmtn label" (cerebral cortex). In
other
instances, although there are a small number of skull voxels that were
not
removed automatically, these voxels do not have an associated "sgmnt
label"
available in TkMedit Tools.
Is it the case that only the voxels for which there is a segmentation
label
are actually added to the total grey volume estimate??
Thus, voxels, which have not been automatically labelled would not
impact
volume computations?
Thank you kindly for your help.
Message: 3 Date: Sun, 5 Jan 2014 15:55:13 -0500 (EST) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Motion correction for SPACE FLAIR To: Octavian Lie octavian.lie@gmail.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.03.1401051554470.16518@nmr.mgh.harvard.edu Content-Type: text/plain; charset="windows-1252"
Hi Octavian
it's not so easy to reduce the bandwidth in the T2-space sequences, but certainly you can try. Geometry-matched just means that the FOV and matrix sizes are the same.
cheers Bruce On Fri, 3 Jan 2014, Octavian Lie wrote:
Dear Bruce,
Best wishes for 2014!
I will heed your advice and cc to the list. Indeed, the MGH protocol I obtained from Andre has one acquisition (NSA). Related, I cc this post:
We have been trying adaptations of the T2spaceFLAIR MGH protocol on our Phillips 3T scanners (sequences called VISTA). Incorporation of the T2 space FLAIR has been mostly successful at editing out the dura from the pial surface. The only concern are minute differences occasionally appearing as small indentations (at most times <1-2mm) between the woFLAIR.pial and the final pial surfaces, including in intrasulcal (duraless) areas; the amount of these small mismatches is variable from patient to patients, with some trials with almost perfect overlap, and others with visible, if small, differences. I wonder if this has been your experience too, and if this is due mostly to bb registration limits or to differences in pixel bandwidth between mprage and space flair sequences (in our case, see below). In FSwiki, the recommendation is that T2 space flair ?should be bandwidth, geometry and readout matched to the mprage?.
- Speaking about pixel bandwidth, logistics most likely would not
allow application of a MEMPR sequence on our Phillips. According to Siemens MPRAGE MGH specs, "exceptions indicate that if a multiple echo sequence is not available, one should choose a bandwidth of 195 Hz/pixel for the MPRAGE". In that case/ using the Siemens Trio MPRAGE protocol as if the MEMPR is not available, how one would adjust the bandwidth in T2spaceFLAIR protocol (currently ~650 in the Siemens space flair and MEMPR protocols) to "match" it to the "simple" MPRAGE protocol (decreasing it to 195 ?). Would it be a workaround? (Please comment on the Siemens case, obviously, I do not expect any light on Phillips without further testing). 2. Could you clarify what geometry matched means? Please advise,
Thank you,
Octavian
On Fri, Jan 3, 2014 at 9:12 PM, Bruce Fischl
fischl@nmr.mgh.harvard.edu wrote:
Hi Octavian
can you cc the list so that others can answer? What is NSA? We don't
have a
ton of experience with it, but 1 has seemed ok (not sure if we've ever
tried
two) Bruce
On Thu, 2 Jan 2014, Octavian Lie wrote:
Dear Bruce,
Thank you. We used one vs 2 NSA T2 space FLAIR sequences, without a consistent difference in results, with the 2-NSA run obviously
doubling
the scan time. Is there a preferred number of NSA you recommend, or we
should
be fine with one? Both are at resolution 1X1X1 mm. Thank you,
Octavian
On Thu, Jan 2, 2014 at 11:56 AM, Bruce Fischl
wrote: Hi Octaviaan no, not really. You should motion correct and average them using something like mri_motion_correct*
We do typically bandwidth/readout match them to the memprages so that there is no differential distortion
cheers Bruce
On Wed, 1 Jan 2014, Octavian Lie wrote:
Dear All,
We recently implemented pial correction using T2 space FLAIR with freesurfer v 5.3, mostly successfully. We use 2-3 MPRAGE (sagittal + axial and/or coronal) volumes as 001.mgz, 002/003.mgz for the motion correction step in recon-all pipeline. The typical times for acquiring space FLAIR in our settings vary from 2.5 to 6 min, depending on the resolution/NSA no. I was wondering how freesurfer deals with motion artifacts in the space FLAIR sequence (especially with longer acquisition times), and if there is a strategy to minimize motion distortion with these (such as getting second runs for averaging, etc). Please advise,
Octavian.
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Message: 4 Date: Sun, 5 Jan 2014 19:25:53 -0500 From: Yuliya Yoncheva yuliya.yoncheva@gmail.com Subject: Re: [Freesurfer] erroneuos segmentation labeling of skull outside of brain To: Bruce Fischl fischl@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: CAGE5uFcchoLxBvaf5Lze9z9_QPU4NGa83WFwZ90auZX3-idsFg@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"
Hello Bruce,
thank you very much for your fast response and clarifying that potential voxels outside the pial surface do not impact cortical measures.
Best, Yuliya
On Sun, Jan 5, 2014 at 3:40 PM, Bruce Fischl
fischl@nmr.mgh.harvard.eduwrote:
Hi Yuliya
they are included if they are inside of the ?h.pial surface. We don't
use
the cortex aseg label as it is in general less accurate than the
surfaces.
cheers Bruce
On Sun, 5 Jan 2014, Yuliya Yoncheva wrote:
Dear FreeSurfer community,
I am visually inspecting the quality of my recon -all output for a
large
dataset and have a rookie question.
In some instances, when skull stripping ended up leaving some of the skull, these voxels are associated with a "sgmtn label" (cerebral cortex). In other instances, although there are a small number of skull voxels that were
not
removed automatically, these voxels do not have an associated "sgmnt label" available in TkMedit Tools.
Is it the case that only the voxels for which there is a segmentation label are actually added to the total grey volume estimate?
Thus, voxels, which have not been automatically labelled would not
impact
volume computations?
Thank you kindly for your help.
The information in this e-mail is intended only for the person to whom
it
is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you
in
error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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Message: 5 Date: Sun, 5 Jan 2014 20:29:06 -0500 (EST) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] erroneuos segmentation labeling of skull outside of brain To: Yuliya Yoncheva yuliya.yoncheva@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.03.1401052028520.16518@nmr.mgh.harvard.edu Content-Type: text/plain; charset="iso-8859-1"
exactly, or measures derived them them like whole-brain volume
cheers Bruce
On Sun, 5 Jan 2014, Yuliya Yoncheva wrote:
Hello Bruce, thank you very much for your fast response and clarifying that potential voxels outside the pial surface do not impact cortical measures.
Best,? Yuliya
On Sun, Jan 5, 2014 at 3:40 PM, Bruce Fischl
wrote: Hi Yuliya
they are included if they are inside of the ?h.pial surface. We don't use the cortex aseg label as it is in general less accurate than the surfaces.
cheers Bruce On Sun, 5 Jan 2014, Yuliya Yoncheva wrote:
Dear FreeSurfer community, I am visually inspecting the quality of my recon -all output for a large dataset and have a rookie question.
In some instances, when skull stripping ended up leaving some of the skull, these voxels are associated with a "sgmtn label" (cerebral cortex). In other instances, although there are a small number of skull voxels that were not removed automatically, these voxels do not have an associated "sgmnt label" available in TkMedit Tools.
Is it the case that only the voxels for which there is a segmentation label are actually added to the total grey volume estimate??
Thus, voxels, which have not been automatically labelled would not impact volume computations?
Thank you kindly for your help.
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Message: 6 Date: Sun, 5 Jan 2014 20:50:51 -0500 (EST) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all exited w/errors To: "Boric, Katica A." KBORIC@mgh.harvard.edu Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.03.1401052049480.16518@nmr.mgh.harvard.edu Content-Type: text/plain; charset="iso-8859-1"
Hi Katica
what format was the input image to recon-all? Can you verify that tkmedit has the directions correct (that is what it labels as anterior is actually anatomically anterior, etc...). If so, then the talairach just failed and you will need to either try an alternative (like the MNI or SPM
talairachs)
or generate it manually.
cheers Bruce
On Thu, 2 Jan 2014, Boric, Katica A. wrote:
Happy New Year freesuerfers! I run into this error while doing?recon-all :
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string.
I would really appreciate if someone could give me some advice on how to
fix
this error.
Thank you very much!
Katica Boric,
ps:?Here is the error log:
#@# Talairach Failure Detection Thu Jan ?2 14:20:32 EST 2014 /home/XX/XXX/subjects/XXX_SurferOutput/mri
?talairach_afd -T 0.005 -xfm transforms/talairach.xfm?
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) INFO: Attempting MINC mritotal to perform Talairach align #-------------------------------------------- #@# Talairach Thu Jan ?2 14:20:33 EST 2014 /home/XX/XXX/subjects/XXX_SurferOutput/mri
?mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale
--i
orig.mgz --o orig_nu.mgz?
?talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm?
/home/XX/XXX/subjects/XXX_SurferOutput/mri /usr/local/freesurfer/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8
20:57:42
UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Thu Jan ?2 14:21:30 EST 2014 tmpdir is transforms/tmp.talairach.34005 /home/XX/XXX/subjects/XXX_SurferOutput/mri mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc? $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=8.23, TE=3.22, TI=450.00, flip angle=12.00 i_ras = (-1, -9.03383e-08, 0) j_ras = (-1.3411e-07, 2.66591e-08, -1) k_ras = (1.59256e-07, 1, -5.93718e-09) writing to transforms/tmp.talairach.34005/src.mnc...
mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.34005/src.mnc transforms/talairach.auto.xfm Legacy library shellwords.pl will be removed from the Perl core
distribution
in the next major release. Please install it from the CPAN distribution Perl4::CoreLibs. It is being used at
/usr/local/freesurfer/mni/bin/mritotal,
line 460. ? ? Thu Jan ?2 14:21:43 EST 2014 talairach done
?cp transforms/talairach.auto.xfm transforms/talairach.xfm?
#-------------------------------------------- #@# Talairach Failure Detection Thu Jan ?2 14:21:44 EST 2014 /home/XX/XXX/subjects/XXX_SurferOutput/mri
?talairach_afd -T 0.005 -xfm transforms/talairach.xfm?
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8
20:57:42
UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s xxx_SurferOutput exited with ERRORS at Thu Jan ?2 14:21:45
EST
2014
Message: 7 Date: Sun, 5 Jan 2014 23:35:55 -0800 From: Frank Hsieh two.frank@gmail.com Subject: [Freesurfer] ROI masks created in FreeSurfer used in FSL?? To: freesurfer@nmr.mgh.harvard.edu Message-ID: CABBeRCEt37ZwE1-jHuZGC3Vw-D_v2+svOAnQUcSP6kW37qT4oQ@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"
Dear FreeSurfer Users,
I ran recon -all on my structural image and created ROI masks (using mri_label2vol) based on FreeSurfer's cortical parcellation. I'd like to
use
these masks for further analysis with FSL. However, it seems that the ROI masks generated with mri_label2vol have different header information than that of the original structural image. As a result, I was unable to carry out further analysis with FSL (e.g., converting these ROI masks into functional space with hires2example_func.mat). I was wondering if there is a way to solve this issue.
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Message: 8 Date: Mon, 6 Jan 2014 17:11:54 +0900 From: Muhammad Naveed Iqbal Qureshi mniqureshi@hotmail.com Subject: [Freesurfer] converting .thickness files of T1 MRI from FreeSurfer into AFNI To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: BLU174-W27296B6C59F4D34F89293AC4B70@phx.gbl Content-Type: text/plain; charset="ks_c_5601-1987"
Hi, I want to know that how can I convert FreeSurfer .thickness files to AFNI
readable format
I tried the following Command but it gives error
mri_convert /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness
/media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to
/media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik...
AFNI BRIK write unsupported ERROR: failure writing
/media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik
UN:/media>
Please let me help me to solve this problem Thank you :)
Best Regards,
Muhammad Naveed Iqbal Qureshi
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Message: 9 Date: Mon, 6 Jan 2014 10:45:52 +0100 From: "L. Schweren" l.j.s.schweren@umcg.nl Subject: [Freesurfer] brain orientation in qdec To: freesurfer@nmr.mgh.harvard.edu Message-ID: 005601cf0ac4$16bda9b0$4438fd10$@umcg.nl Content-Type: text/plain; charset="us-ascii"
Dear experts,
I ran recon-all with qcache. When loading the right hemisphere of
fsaverage
(or any other surface reconstruction) into tksurfer (for example command: tksurfer fsaverage rh white), the left hemisphere surface is displayed,
and
it is upside down. When I import annotations they load in the same orientation as the surface. However, the coordinates and the labels, displayed in the Tksurfer Tools window, are not. For example, when I move the cursor to the temporal lobe, the label says it's postcentral. I do not mind manually turning the surfaces in tksurfer, but I do need to be sure I am looking at the correct hemispheres, coordinates and labels.
I hope you can help me solve this. Thank you in advance.
Best wishes,
Lizanne
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Message: 10 Date: Mon, 6 Jan 2014 08:41:58 -0500 (EST) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] converting .thickness files of T1 MRI from FreeSurfer into AFNI To: Muhammad Naveed Iqbal Qureshi mniqureshi@hotmail.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.03.1401060840550.16518@nmr.mgh.harvard.edu Content-Type: text/plain; charset="iso-8859-15"
Hi Muhammad
try:
set sdir=/home/naveed/freesurfer/subjects/CHR01/surf mris_convert -c $sdir/rh.thickness $sdir/rh.orig $sdir/rh.thickness.brik
cheers Bruce
On Mon, 6 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Hi, I want to know that how can I convert FreeSurfer .thickness files to
AFNI
readable format I tried the following Command but it gives error
mri_convert /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to
/media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik...
AFNI BRIK write unsupported ERROR: failure writing /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik UN:/media>
Please let me help me to solve this problem Thank you :)?
Best Regards, Muhammad Naveed Iqbal Qureshi
Message: 11 Date: Mon, 6 Jan 2014 10:40:43 -0500 (EST) From: "Emad Ahmadi" emad@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all error To: freesurfer@nmr.mgh.harvard.edu Message-ID: 63234.172.19.2.113.1389022843.squirrel@mail.martinos.org Content-Type: text/plain; charset="iso-8859-1"
Hello & Happy New Year!
I'm running recon-all for one subject on MGH clusters (ERISone), and it exits with error. I would appreciate it if you help me figure out what the problem is. The log file is attached.
All the best throughout 2014! Emad
Emad Ahmadi, MD
Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School
25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: emad@nmr.mgh.harvard.edu
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Message: 12 Date: Mon, 6 Jan 2014 17:51:18 +0200 From: Rotem Saar saar.rotem@gmail.com Subject: [Freesurfer] Fwd: Anatomical segmentation - question To: freesurfer@nmr.mgh.harvard.edu Message-ID: CAMjFEmbcEwbXMOyxw-kuep6NSzdnk=rYHSEvwPGSbiXkBZKxtA@mail.gmail.com Content-Type: text/plain; charset="windows-1252"
Dear freesurfer experts,
I'm performing anatomical segmentation for Philips dicoms (3T scanner). I got these two images from the same slice while performing step number 4 in the script below ? from some reason, the two images don't fit. Should I
use
"scale brain" ? I know this is not recommended thus want to consult with u first ? Can u please comment on why this is happening? Is there any value that corresponds to "how good is the segmentation" ? if yes, where can I find it ?
My script is written below.
Thanks,
Rotem
Anatomical segmentation:
first step- 23 hours:
*recon-all -autorecon-all -i ~/Desktop/ FOLDER-NAME /I00001.dcm -s FOLDER-NAME*
second step:(gyrus=green, sulcus=red)
*tksurfer -curv FOLDER-NAME lh/rh inflated*
third step: (talairch registretion)
*tkmedit FOLDER-NAME brainmask.mgz*
File-> transforms-> load transform AUX-> Browse-> talairch.xfm
forth step: (simetry - allows changing 12df transformation. if we made any changes we should click "save reg" and run this command again)
*tkregister2 --mgz --s FOLDER-NAME --fstal --surf orig*
IF WE CHANGE ANYTHING, CLICK "SAVE REG" AND RUN FROM STARTING POING: recon-all -all -subjectid FOLDER-NAME
fifth step: (scalp removal: if removed too much, rise up from the value
25:
*recon-all -skullstrip -wsthresh 25 -clean-bm -no-wsgcaatlas -s FOLDER-NAME *
to check the result press: *tkmedit FOLDER-NAME brainmask.mgz lh.white
-aux
T1.mgz -aux-surface rh.white *)
for hand correction: *tkmedit FOLDER-NAME brainmask.mgz -aux T1.mgz*
tools-> configure volume brush -> MARK: mode=clone, source=Aux
tools-> configure brush info (for choosing brush size)
click on edit voxels: click in MIDDLE for adding voxels, RIGHT for
removing
voxels : slice by slice.
when finish, click: File-> save main volume
sisxt step: (cp for correcting segmentation)
*tkmedit FOLDER-NAME brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white*
seventh step: (done)
*recon-all -autorecon2-cp -autorecon3 -s FOLDER-NAME*
Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev Beer-Sheva 84105 Israel -------------- next part -------------- An HTML attachment was scrubbed... URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140106/3
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
End of Freesurfer Digest, Vol 119, Issue 6
try adding "paint" after "surf/rh.thickness". The -surfval switch takes an optional format parameter after the file name I think
cheers Bruce
On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Hi Bruce, I have tried to convert by using the following commands but still some error occur. UN:~> set subj=/home/naveed/freesurfer/subjects/CHR01/ UN:~> mri_surf2vol --surfval surf/rh.thickness --hemi rh --fillribbon --template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii gdiagno = -1 ERROR: cannot recognize the type of surf/rh.thickness
Can you help me. Thank you.
Best Regards, Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:13:45 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
Hi Muhammad
have you looked at the help? It's pretty extensive. If you have trouble post again and Doug should be able to guide you
cheers Bruce On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Thank you Bruce, Please guide me how can I use mri_surf2vol command on lh/rh.thickness
files
to get the output as lh/rh.ribbon.nii for AFNI SUMA. Thank you
Best Regards, Muhammad Naveed Iqbal Qureshi
From: freesurfer-request@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 119, Issue 6 To: freesurfer@nmr.mgh.harvard.edu Date: Mon, 6 Jan 2014 10:51:33 -0500
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
- erroneuos segmentation labeling of skull outside of brain
(Yuliya Yoncheva) 2. Re: erroneuos segmentation labeling of skull outside of brain (Bruce Fischl) 3. Re: Motion correction for SPACE FLAIR (Bruce Fischl) 4. Re: erroneuos segmentation labeling of skull outside of brain (Yuliya Yoncheva) 5. Re: erroneuos segmentation labeling of skull outside of brain (Bruce Fischl) 6. Re: recon-all exited w/errors (Bruce Fischl) 7. ROI masks created in FreeSurfer used in FSL?? (Frank Hsieh) 8. converting .thickness files of T1 MRI from FreeSurfer into AFNI (Muhammad Naveed Iqbal Qureshi) 9. brain orientation in qdec (L. Schweren) 10. Re: converting .thickness files of T1 MRI from FreeSurfer into AFNI (Bruce Fischl) 11. recon-all error (Emad Ahmadi) 12. Fwd: Anatomical segmentation - question (Rotem Saar)
Message: 1 Date: Sun, 5 Jan 2014 15:14:39 -0500 From: Yuliya Yoncheva yuliya.yoncheva@gmail.com Subject: [Freesurfer] erroneuos segmentation labeling of skull outside of brain To: freesurfer@nmr.mgh.harvard.edu Message-ID: CAGE5uFc2uD9pMefXjRZE0LQP+GcfhHKWeVkHxOGwDzV1=jYrQA@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"
Dear FreeSurfer community,
I am visually inspecting the quality of my recon -all output for a
large
dataset and have a rookie question.
In some instances, when skull stripping ended up leaving some of the
skull,
these voxels are associated with a "sgmtn label" (cerebral cortex). In other instances, although there are a small number of skull voxels
that
were not removed automatically, these voxels do not have an associated "sgmnt label" available in TkMedit Tools.
Is it the case that only the voxels for which there is a segmentation
label
are actually added to the total grey volume estimate?
Thus, voxels, which have not been automatically labelled would not
impact
volume computations?
Thank you kindly for your help.
Still the same error
UN:~> mri_surf2vol --surfval surf/rh.thickness.paint --hemi rh --fillribbon --template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii gdiagno = -1 ERROR: cannot recognize the type of surf/rh.thickness.paint
Best Regards,
Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:20:43 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
try adding "paint" after "surf/rh.thickness". The -surfval switch takes an optional format parameter after the file name I think
cheers Bruce
On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Hi Bruce, I have tried to convert by using the following commands but still some error occur.
UN:~> set subj=/home/naveed/freesurfer/subjects/CHR01/ UN:~> mri_surf2vol --surfval surf/rh.thickness --hemi rh --fillribbon --template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii gdiagno = -1 ERROR: cannot recognize the type of surf/rh.thickness
Can you help me. Thank you.
Best Regards, Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:13:45 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
Hi Muhammad
have you looked at the help? It's pretty extensive. If you have trouble post again and Doug should be able to guide you
cheers Bruce On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Thank you Bruce,
Please guide me how can I use mri_surf2vol command on lh/rh.thickness
files
to get the output as lh/rh.ribbon.nii for AFNI SUMA. Thank you
Best Regards, Muhammad Naveed Iqbal Qureshi
From: freesurfer-request@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 119, Issue 6 To: freesurfer@nmr.mgh.harvard.edu Date: Mon, 6 Jan 2014 10:51:33 -0500
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
- erroneuos segmentation labeling of skull outside of brain
(Yuliya Yoncheva) 2. Re: erroneuos segmentation labeling of skull outside of brain (Bruce Fischl) 3. Re: Motion correction for SPACE FLAIR (Bruce Fischl) 4. Re: erroneuos segmentation labeling of skull outside of brain (Yuliya Yoncheva) 5. Re: erroneuos segmentation labeling of skull outside of brain (Bruce Fischl) 6. Re: recon-all exited w/errors (Bruce Fischl) 7. ROI masks created in FreeSurfer used in FSL?? (Frank Hsieh) 8. converting .thickness files of T1 MRI from FreeSurfer into AFNI (Muhammad Naveed Iqbal Qureshi) 9. brain orientation in qdec (L. Schweren) 10. Re: converting .thickness files of T1 MRI from FreeSurfer into AFNI (Bruce Fischl) 11. recon-all error (Emad Ahmadi) 12. Fwd: Anatomical segmentation - question (Rotem Saar)
Message: 1 Date: Sun, 5 Jan 2014 15:14:39 -0500 From: Yuliya Yoncheva yuliya.yoncheva@gmail.com Subject: [Freesurfer] erroneuos segmentation labeling of skull outside of brain To: freesurfer@nmr.mgh.harvard.edu Message-ID: CAGE5uFc2uD9pMefXjRZE0LQP+GcfhHKWeVkHxOGwDzV1=jYrQA@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"
Dear FreeSurfer community,
I am visually inspecting the quality of my recon -all output for a
large
dataset and have a rookie question.
In some instances, when skull stripping ended up leaving some of the
skull,
these voxels are associated with a "sgmtn label" (cerebral cortex). In other instances, although there are a small number of skull voxels
that
were not removed automatically, these voxels do not have an associated "sgmnt label" available in TkMedit Tools.
Is it the case that only the voxels for which there is a segmentation
label
are actually added to the total grey volume estimate?
Thus, voxels, which have not been automatically labelled would not
impact
volume computations?
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Message: 2 Date: Sun, 5 Jan 2014 15:40:24 -0500 (EST) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] erroneuos segmentation labeling of skull outside of brain To: Yuliya Yoncheva yuliya.yoncheva@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.03.1401051539450.16518@nmr.mgh.harvard.edu Content-Type: text/plain; charset="iso-8859-1"
Hi Yuliya
they are included if they are inside of the ?h.pial surface. We don't
use
the cortex aseg label as it is in general less accurate than the
surfaces.
cheers Bruce On Sun, 5 Jan 2014, Yuliya Yoncheva wrote:
Dear FreeSurfer community, I am visually inspecting the quality of my recon -all output for a
large
dataset and have a rookie question.
In some instances, when skull stripping ended up leaving some of the
skull,
these voxels are associated with a "sgmtn label" (cerebral cortex).
In
other
instances, although there are a small number of skull voxels that
were
not
removed automatically, these voxels do not have an associated "sgmnt
label"
available in TkMedit Tools.
Is it the case that only the voxels for which there is a
segmentation
label
are actually added to the total grey volume estimate??
Thus, voxels, which have not been automatically labelled would not
impact
volume computations?
Thank you kindly for your help.
Message: 3 Date: Sun, 5 Jan 2014 15:55:13 -0500 (EST) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Motion correction for SPACE FLAIR To: Octavian Lie octavian.lie@gmail.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.03.1401051554470.16518@nmr.mgh.harvard.edu Content-Type: text/plain; charset="windows-1252"
Hi Octavian
it's not so easy to reduce the bandwidth in the T2-space sequences,
but
certainly you can try. Geometry-matched just means that the FOV and matrix sizes are the same.
cheers Bruce On Fri, 3 Jan 2014, Octavian Lie wrote:
Dear Bruce,
Best wishes for 2014!
I will heed your advice and cc to the list. Indeed, the MGH protocol
I
obtained from Andre has one acquisition (NSA). Related, I cc this post:
We have been trying adaptations of the T2spaceFLAIR MGH protocol on our Phillips 3T scanners (sequences called VISTA). Incorporation of the T2 space FLAIR has been mostly successful at editing out the
dura
from the pial surface. The only concern are minute differences occasionally appearing as small indentations (at most times <1-2mm) between the woFLAIR.pial and the final pial surfaces, including in intrasulcal (duraless) areas; the amount of these small mismatches
is
variable from patient to patients, with some trials with almost perfect overlap, and others with visible, if small, differences. I wonder if this has been your experience too, and if this is due
mostly
to bb registration limits or to differences in pixel bandwidth
between
mprage and space flair sequences (in our case, see below). In FSwiki, the recommendation is that T2 space flair ?should be bandwidth, geometry and readout matched to the mprage?.
- Speaking about pixel bandwidth, logistics most likely would not
allow application of a MEMPR sequence on our Phillips. According to Siemens MPRAGE MGH specs, "exceptions indicate that if a multiple
echo
sequence is not available, one should choose a bandwidth of 195 Hz/pixel for the MPRAGE". In that case/ using the Siemens Trio
MPRAGE
protocol as if the MEMPR is not available, how one would adjust the bandwidth in T2spaceFLAIR protocol (currently ~650 in the Siemens space flair and MEMPR protocols) to "match" it to the "simple"
MPRAGE
protocol (decreasing it to 195 ?). Would it be a workaround? (Please comment on the Siemens case, obviously, I do not expect any light on Phillips without further testing). 2. Could you clarify what geometry matched means? Please advise,
Thank you,
Octavian
On Fri, Jan 3, 2014 at 9:12 PM, Bruce Fischl
fischl@nmr.mgh.harvard.edu wrote:
> Hi Octavian > > can you cc the list so that others can answer? What is NSA? We
don't
have a
> ton of experience with it, but 1 has seemed ok (not sure if we've
ever
tried
> two) > Bruce > > > > On Thu, 2 Jan 2014, Octavian Lie wrote: > >> Dear Bruce, >> >> Thank you. We used one vs 2 NSA T2 space FLAIR sequences, without
a
>> consistent difference in results, with the 2-NSA run obviously
doubling
>> the >> scan time. Is there a preferred number of NSA you recommend, or we
should
>> be >> fine with one? Both are at resolution 1X1X1 mm. >> Thank you, >> >> Octavian >> >> >> >> On Thu, Jan 2, 2014 at 11:56 AM, Bruce Fischl
>> wrote: >> Hi Octaviaan >> no, not really. You should motion correct and average them using >> something like mri_motion_correct* >> >> We do typically bandwidth/readout match them to the memprages so >> that there is no differential distortion >> >> cheers >> Bruce >> >> >> On Wed, 1 Jan 2014, Octavian Lie wrote: >> >> Dear All, >> >> We recently implemented pial correction using T2 >> space FLAIR with freesurfer >> v 5.3, mostly successfully. We use 2-3 MPRAGE >> (sagittal + axial and/or >> coronal) volumes as 001.mgz, 002/003.mgz for the >> motion correction step in >> recon-all pipeline. >> The typical times for acquiring space FLAIR in our >> settings vary from 2.5 to >> 6 min, depending on the resolution/NSA no. I was >> wondering how freesurfer >> deals with motion artifacts in the space FLAIR >> sequence (especially with >> longer acquisition times), and if there is a >> strategy to minimize motion >> distortion with these (such as getting second runs >> for averaging, etc). >> Please advise, >> >> Octavian. >> >> >> >> >> The information in this e-mail is intended only for the person to
whom
>> it is >> addressed. If you believe this e-mail was sent to you in error and
the
>> e-mail >> contains patient information, please contact the Partners
Compliance
>> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to
you
>> in error >> but does not contain patient information, please contact the
sender
>> and properly >> dispose of the e-mail. >> >> >> >
Message: 4 Date: Sun, 5 Jan 2014 19:25:53 -0500 From: Yuliya Yoncheva yuliya.yoncheva@gmail.com Subject: Re: [Freesurfer] erroneuos segmentation labeling of skull outside of brain To: Bruce Fischl fischl@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: CAGE5uFcchoLxBvaf5Lze9z9_QPU4NGa83WFwZ90auZX3-idsFg@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"
Hello Bruce,
thank you very much for your fast response and clarifying that
potential
voxels outside the pial surface do not impact cortical measures.
Best, Yuliya
On Sun, Jan 5, 2014 at 3:40 PM, Bruce Fischl
fischl@nmr.mgh.harvard.eduwrote:
Hi Yuliya
they are included if they are inside of the ?h.pial surface. We
don't
use
the cortex aseg label as it is in general less accurate than the
surfaces.
cheers Bruce
On Sun, 5 Jan 2014, Yuliya Yoncheva wrote:
Dear FreeSurfer community, > I am visually inspecting the quality of my recon -all output for a
large
> dataset and have a rookie question. > > In some instances, when skull stripping ended up leaving some of
the
> skull, > these voxels are associated with a "sgmtn label" (cerebral cortex).
In
> other > instances, although there are a small number of skull voxels that
were
not
> removed automatically, these voxels do not have an associated
"sgmnt
> label" > available in TkMedit Tools. > > Is it the case that only the voxels for which there is a
segmentation
> label > are actually added to the total grey volume estimate? > > Thus, voxels, which have not been automatically labelled would not
impact
> volume computations? > > Thank you kindly for your help. > > >
The information in this e-mail is intended only for the person to
whom
it
is addressed. If you believe this e-mail was sent to you in error and
the
e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to
you
in
error but does not contain patient information, please contact the sender
and
properly dispose of the e-mail.
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Message: 5 Date: Sun, 5 Jan 2014 20:29:06 -0500 (EST) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] erroneuos segmentation labeling of skull outside of brain To: Yuliya Yoncheva yuliya.yoncheva@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.03.1401052028520.16518@nmr.mgh.harvard.edu Content-Type: text/plain; charset="iso-8859-1"
exactly, or measures derived them them like whole-brain volume
cheers Bruce
On Sun, 5 Jan 2014, Yuliya Yoncheva wrote:
Hello Bruce, thank you very much for your fast response and clarifying that
potential
voxels outside the pial surface do not impact cortical measures.
Best,? Yuliya
On Sun, Jan 5, 2014 at 3:40 PM, Bruce Fischl
wrote: Hi Yuliya
they are included if they are inside of the ?h.pial surface. We don't use the cortex aseg label as it is in general less accurate than the surfaces.
cheers Bruce On Sun, 5 Jan 2014, Yuliya Yoncheva wrote:
Dear FreeSurfer community, I am visually inspecting the quality of my recon -all output for a large dataset and have a rookie question.
In some instances, when skull stripping ended up leaving some of the skull, these voxels are associated with a "sgmtn label" (cerebral cortex). In other instances, although there are a small number of skull voxels that were not removed automatically, these voxels do not have an associated "sgmnt label" available in TkMedit Tools.
Is it the case that only the voxels for which there is a segmentation label are actually added to the total grey volume estimate??
Thus, voxels, which have not been automatically labelled would not impact volume computations?
Thank you kindly for your help.
The information in this e-mail is intended only for the person to
whom
it is addressed. If you believe this e-mail was sent to you in error and
the
e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to
you
in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Message: 6 Date: Sun, 5 Jan 2014 20:50:51 -0500 (EST) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all exited w/errors To: "Boric, Katica A." KBORIC@mgh.harvard.edu Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.03.1401052049480.16518@nmr.mgh.harvard.edu Content-Type: text/plain; charset="iso-8859-1"
Hi Katica
what format was the input image to recon-all? Can you verify that
tkmedit
has the directions correct (that is what it labels as anterior is
actually
anatomically anterior, etc...). If so, then the talairach just failed
and
you will need to either try an alternative (like the MNI or SPM
talairachs)
or generate it manually.
cheers Bruce
On Thu, 2 Jan 2014, Boric, Katica A. wrote:
Happy New Year freesuerfers! I run into this error while doing?recon-all :
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string.
I would really appreciate if someone could give me some advice on
how to
fix
this error.
Thank you very much!
Katica Boric,
ps:?Here is the error log:
#@# Talairach Failure Detection Thu Jan ?2 14:20:32 EST 2014 /home/XX/XXX/subjects/XXX_SurferOutput/mri
?talairach_afd -T 0.005 -xfm transforms/talairach.xfm?
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) INFO: Attempting MINC mritotal to perform Talairach align #-------------------------------------------- #@# Talairach Thu Jan ?2 14:20:33 EST 2014 /home/XX/XXX/subjects/XXX_SurferOutput/mri
?mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50
--no-rescale
--i
orig.mgz --o orig_nu.mgz?
?talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm?
/home/XX/XXX/subjects/XXX_SurferOutput/mri /usr/local/freesurfer/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8
20:57:42
UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Thu Jan ?2 14:21:30 EST 2014 tmpdir is transforms/tmp.talairach.34005 /home/XX/XXX/subjects/XXX_SurferOutput/mri mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc? $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=8.23, TE=3.22, TI=450.00, flip angle=12.00 i_ras = (-1, -9.03383e-08, 0) j_ras = (-1.3411e-07, 2.66591e-08, -1) k_ras = (1.59256e-07, 1, -5.93718e-09) writing to transforms/tmp.talairach.34005/src.mnc...
mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.34005/src.mnc transforms/talairach.auto.xfm Legacy library shellwords.pl will be removed from the Perl core
distribution
in the next major release. Please install it from the CPAN
distribution
Perl4::CoreLibs. It is being used at
/usr/local/freesurfer/mni/bin/mritotal,
line 460. ? ? Thu Jan ?2 14:21:43 EST 2014 talairach done
?cp transforms/talairach.auto.xfm transforms/talairach.xfm?
#-------------------------------------------- #@# Talairach Failure Detection Thu Jan ?2 14:21:44 EST 2014 /home/XX/XXX/subjects/XXX_SurferOutput/mri
?talairach_afd -T 0.005 -xfm transforms/talairach.xfm?
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8
20:57:42
UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s xxx_SurferOutput exited with ERRORS at Thu Jan ?2
14:21:45
EST
2014
Message: 7 Date: Sun, 5 Jan 2014 23:35:55 -0800 From: Frank Hsieh two.frank@gmail.com Subject: [Freesurfer] ROI masks created in FreeSurfer used in FSL?? To: freesurfer@nmr.mgh.harvard.edu Message-ID: CABBeRCEt37ZwE1-jHuZGC3Vw-D_v2+svOAnQUcSP6kW37qT4oQ@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"
Dear FreeSurfer Users,
I ran recon -all on my structural image and created ROI masks (using mri_label2vol) based on FreeSurfer's cortical parcellation. I'd like
to
use
these masks for further analysis with FSL. However, it seems that the
ROI
masks generated with mri_label2vol have different header information
than
that of the original structural image. As a result, I was unable to
carry
out further analysis with FSL (e.g., converting these ROI masks into functional space with hires2example_func.mat). I was wondering if
there is
a way to solve this issue.
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Message: 8 Date: Mon, 6 Jan 2014 17:11:54 +0900 From: Muhammad Naveed Iqbal Qureshi mniqureshi@hotmail.com Subject: [Freesurfer] converting .thickness files of T1 MRI from FreeSurfer into AFNI To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: BLU174-W27296B6C59F4D34F89293AC4B70@phx.gbl Content-Type: text/plain; charset="ks_c_5601-1987"
Hi, I want to know that how can I convert FreeSurfer .thickness files to
AFNI
readable format
I tried the following Command but it gives error
mri_convert /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness
/media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from
/home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to
/media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik...
AFNI BRIK write unsupported ERROR: failure writing
/media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik
UN:/media>
Please let me help me to solve this problem Thank you :)
Best Regards,
Muhammad Naveed Iqbal Qureshi
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Message: 9 Date: Mon, 6 Jan 2014 10:45:52 +0100 From: "L. Schweren" l.j.s.schweren@umcg.nl Subject: [Freesurfer] brain orientation in qdec To: freesurfer@nmr.mgh.harvard.edu Message-ID: 005601cf0ac4$16bda9b0$4438fd10$@umcg.nl Content-Type: text/plain; charset="us-ascii"
Dear experts,
I ran recon-all with qcache. When loading the right hemisphere of
fsaverage
(or any other surface reconstruction) into tksurfer (for example
command:
tksurfer fsaverage rh white), the left hemisphere surface is
displayed,
and
it is upside down. When I import annotations they load in the same orientation as the surface. However, the coordinates and the labels, displayed in the Tksurfer Tools window, are not. For example, when I
move
the cursor to the temporal lobe, the label says it's postcentral. I do
not
mind manually turning the surfaces in tksurfer, but I do need to be
sure I
am looking at the correct hemispheres, coordinates and labels.
I hope you can help me solve this. Thank you in advance.
Best wishes,
Lizanne
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Message: 10 Date: Mon, 6 Jan 2014 08:41:58 -0500 (EST) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] converting .thickness files of T1 MRI from FreeSurfer into AFNI To: Muhammad Naveed Iqbal Qureshi mniqureshi@hotmail.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.03.1401060840550.16518@nmr.mgh.harvard.edu Content-Type: text/plain; charset="iso-8859-15"
Hi Muhammad
try:
set sdir=/home/naveed/freesurfer/subjects/CHR01/surf mris_convert -c $sdir/rh.thickness $sdir/rh.orig
$sdir/rh.thickness.brik
cheers Bruce
On Mon, 6 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Hi, I want to know that how can I convert FreeSurfer .thickness files to
AFNI
readable format I tried the following Command but it gives error
mri_convert /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from
/home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to
/media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik...
AFNI BRIK write unsupported ERROR: failure writing /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik UN:/media>
Please let me help me to solve this problem Thank you :)?
Best Regards, Muhammad Naveed Iqbal Qureshi
Message: 11 Date: Mon, 6 Jan 2014 10:40:43 -0500 (EST) From: "Emad Ahmadi" emad@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all error To: freesurfer@nmr.mgh.harvard.edu Message-ID: 63234.172.19.2.113.1389022843.squirrel@mail.martinos.org Content-Type: text/plain; charset="iso-8859-1"
Hello & Happy New Year!
I'm running recon-all for one subject on MGH clusters (ERISone), and
it
exits with error. I would appreciate it if you help me figure out what
the
problem is. The log file is attached.
All the best throughout 2014! Emad
Emad Ahmadi, MD
Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School
25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: emad@nmr.mgh.harvard.edu
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Message: 12 Date: Mon, 6 Jan 2014 17:51:18 +0200 From: Rotem Saar saar.rotem@gmail.com Subject: [Freesurfer] Fwd: Anatomical segmentation - question To: freesurfer@nmr.mgh.harvard.edu Message-ID: CAMjFEmbcEwbXMOyxw-kuep6NSzdnk=rYHSEvwPGSbiXkBZKxtA@mail.gmail.com Content-Type: text/plain; charset="windows-1252"
Dear freesurfer experts,
I'm performing anatomical segmentation for Philips dicoms (3T
scanner). I
got these two images from the same slice while performing step number
4 in
the script below ? from some reason, the two images don't fit. Should
I
use
"scale brain" ? I know this is not recommended thus want to consult
with u
first ? Can u please comment on why this is happening? Is there any
value
that corresponds to "how good is the segmentation" ? if yes, where can
I
find it ?
My script is written below.
Thanks,
Rotem
Anatomical segmentation:
first step- 23 hours:
*recon-all -autorecon-all -i ~/Desktop/ FOLDER-NAME /I00001.dcm -s FOLDER-NAME*
second step:(gyrus=green, sulcus=red)
*tksurfer -curv FOLDER-NAME lh/rh inflated*
third step: (talairch registretion)
*tkmedit FOLDER-NAME brainmask.mgz*
File-> transforms-> load transform AUX-> Browse-> talairch.xfm
forth step: (simetry - allows changing 12df transformation. if we made
any
changes we should click "save reg" and run this command again)
*tkregister2 --mgz --s FOLDER-NAME --fstal --surf orig*
IF WE CHANGE ANYTHING, CLICK "SAVE REG" AND RUN FROM STARTING POING: recon-all -all -subjectid FOLDER-NAME
fifth step: (scalp removal: if removed too much, rise up from the
value
25:
*recon-all -skullstrip -wsthresh 25 -clean-bm -no-wsgcaatlas -s FOLDER-NAME *
to check the result press: *tkmedit FOLDER-NAME brainmask.mgz lh.white
-aux
T1.mgz -aux-surface rh.white *)
for hand correction: *tkmedit FOLDER-NAME brainmask.mgz -aux T1.mgz*
tools-> configure volume brush -> MARK: mode=clone, source=Aux
tools-> configure brush info (for choosing brush size)
click on edit voxels: click in MIDDLE for adding voxels, RIGHT for
removing
voxels : slice by slice.
when finish, click: File-> save main volume
sisxt step: (cp for correcting segmentation)
*tkmedit FOLDER-NAME brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white*
seventh step: (done)
*recon-all -autorecon2-cp -autorecon3 -s FOLDER-NAME*
Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev Beer-Sheva 84105 Israel -------------- next part -------------- An HTML attachment was scrubbed... URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/201401
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
End of Freesurfer Digest, Vol 119, Issue 6
sorry, I wasn't clear. Try:
mri_surf2vol --surfval surf/rh.thickness paint --hemi rh --fillribbon \ --template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii
On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Still the same error UN:~> mri_surf2vol --surfval surf/rh.thickness.paint --hemi rh --fillribbon --template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii gdiagno = -1 ERROR: cannot recognize the type of surf/rh.thickness.paint
Best Regards, Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:20:43 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
try adding "paint" after "surf/rh.thickness". The -surfval switch takes an optional format parameter after the file name I think
cheers Bruce
On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Hi Bruce, I have tried to convert by using the following commands but still some
error
occur. UN:~> set subj=/home/naveed/freesurfer/subjects/CHR01/ UN:~> mri_surf2vol --surfval surf/rh.thickness --hemi rh --fillribbon --template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii gdiagno = -1 ERROR: cannot recognize the type of surf/rh.thickness
Can you help me. Thank you.
Best Regards, Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:13:45 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
Hi Muhammad
have you looked at the help? It's pretty extensive. If you have
trouble
post again and Doug should be able to guide you
cheers Bruce On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Thank you Bruce, Please guide me how can I use mri_surf2vol command on
lh/rh.thickness
files
to get the output as lh/rh.ribbon.nii for AFNI SUMA. Thank you
Best Regards, Muhammad Naveed Iqbal Qureshi
From: freesurfer-request@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 119, Issue 6 To: freesurfer@nmr.mgh.harvard.edu Date: Mon, 6 Jan 2014 10:51:33 -0500
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more
specific
than "Re: Contents of Freesurfer digest..."
Today's Topics:
- erroneuos segmentation labeling of skull outside of brain
(Yuliya Yoncheva) 2. Re: erroneuos segmentation labeling of skull outside of brain (Bruce Fischl) 3. Re: Motion correction for SPACE FLAIR (Bruce Fischl) 4. Re: erroneuos segmentation labeling of skull outside of brain (Yuliya Yoncheva) 5. Re: erroneuos segmentation labeling of skull outside of brain (Bruce Fischl) 6. Re: recon-all exited w/errors (Bruce Fischl) 7. ROI masks created in FreeSurfer used in FSL?? (Frank Hsieh) 8. converting .thickness files of T1 MRI from FreeSurfer into AFNI (Muhammad Naveed Iqbal Qureshi) 9. brain orientation in qdec (L. Schweren) 10. Re: converting .thickness files of T1 MRI from FreeSurfer into AFNI (Bruce Fischl) 11. recon-all error (Emad Ahmadi) 12. Fwd: Anatomical segmentation - question (Rotem Saar)
Message: 1 Date: Sun, 5 Jan 2014 15:14:39 -0500 From: Yuliya Yoncheva yuliya.yoncheva@gmail.com Subject: [Freesurfer] erroneuos segmentation labeling of skull
outside
of brain To: freesurfer@nmr.mgh.harvard.edu Message-ID:
CAGE5uFc2uD9pMefXjRZE0LQP+GcfhHKWeVkHxOGwDzV1=jYrQA@mail.gmail.com
Content-Type: text/plain; charset="iso-8859-1"
Dear FreeSurfer community,
I am visually inspecting the quality of my recon -all output for a
large
dataset and have a rookie question.
In some instances, when skull stripping ended up leaving some of
the
skull,
these voxels are associated with a "sgmtn label" (cerebral
cortex). In
other instances, although there are a small number of skull voxels
that
were not removed automatically, these voxels do not have an
associated
"sgmnt label" available in TkMedit Tools.
Is it the case that only the voxels for which there is a
segmentation
label
are actually added to the total grey volume estimate?
Thus, voxels, which have not been automatically labelled would not
impact
volume computations?
Thank you kindly for your help.
Now another error
UN:~> mri_surf2vol --surfval surf/rh.thickness paint --hemi rh --fillribbon --template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii gdiagno = -1 Using identity matrix for registration mghRead(mri/orig.mgz, -1): could not open file mri_surf2vol ERROR: reading mri/orig.mgz header
Best Regards,
Muhammad Naveed Iqbal Qureshi
Ph.D. Candidate
Bio-Medical Signal & System Analysis Laboratory
Department of Medical System Engineering
Gwangju Institute of Sciences and Technology
123, Cheomdangwagi-ro, Buk-gu, Gwangju, 500-712, Republic of Korea
Tel : +82-62-715-3266
Email : mniqureshi@gist.ac.kr
URL : http://bmssa.gist.ac.kr
P please don't print this e-mail unless you really need to
Date: Tue, 7 Jan 2014 08:26:56 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
sorry, I wasn't clear. Try:
mri_surf2vol --surfval surf/rh.thickness paint --hemi rh --fillribbon \ --template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii
On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Still the same error
UN:~> mri_surf2vol --surfval surf/rh.thickness.paint --hemi rh --fillribbon --template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii gdiagno = -1 ERROR: cannot recognize the type of surf/rh.thickness.paint
Best Regards, Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:20:43 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
try adding "paint" after "surf/rh.thickness". The -surfval switch takes an optional format parameter after the file name I think
cheers Bruce
On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Hi Bruce, I have tried to convert by using the following commands but still some
error
occur.
UN:~> set subj=/home/naveed/freesurfer/subjects/CHR01/ UN:~> mri_surf2vol --surfval surf/rh.thickness --hemi rh --fillribbon --template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii gdiagno = -1 ERROR: cannot recognize the type of surf/rh.thickness
Can you help me. Thank you.
Best Regards, Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:13:45 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
Hi Muhammad
have you looked at the help? It's pretty extensive. If you have
trouble
post again and Doug should be able to guide you
cheers Bruce On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Thank you Bruce,
Please guide me how can I use mri_surf2vol command on
lh/rh.thickness
files
to get the output as lh/rh.ribbon.nii for AFNI SUMA. Thank you
Best Regards, Muhammad Naveed Iqbal Qureshi
> From: freesurfer-request@nmr.mgh.harvard.edu > Subject: Freesurfer Digest, Vol 119, Issue 6 > To: freesurfer@nmr.mgh.harvard.edu > Date: Mon, 6 Jan 2014 10:51:33 -0500 > > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner@nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more
specific
> than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. erroneuos segmentation labeling of skull outside of brain > (Yuliya Yoncheva) > 2. Re: erroneuos segmentation labeling of skull outside of brain > (Bruce Fischl) > 3. Re: Motion correction for SPACE FLAIR (Bruce Fischl) > 4. Re: erroneuos segmentation labeling of skull outside of brain > (Yuliya Yoncheva) > 5. Re: erroneuos segmentation labeling of skull outside of brain > (Bruce Fischl) > 6. Re: recon-all exited w/errors (Bruce Fischl) > 7. ROI masks created in FreeSurfer used in FSL?? (Frank Hsieh) > 8. converting .thickness files of T1 MRI from FreeSurfer into > AFNI (Muhammad Naveed Iqbal Qureshi) > 9. brain orientation in qdec (L. Schweren) > 10. Re: converting .thickness files of T1 MRI from FreeSurfer > into AFNI (Bruce Fischl) > 11. recon-all error (Emad Ahmadi) > 12. Fwd: Anatomical segmentation - question (Rotem Saar) > > >
> > Message: 1 > Date: Sun, 5 Jan 2014 15:14:39 -0500 > From: Yuliya Yoncheva yuliya.yoncheva@gmail.com > Subject: [Freesurfer] erroneuos segmentation labeling of skull
outside
> of brain > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: >
CAGE5uFc2uD9pMefXjRZE0LQP+GcfhHKWeVkHxOGwDzV1=jYrQA@mail.gmail.com
> Content-Type: text/plain; charset="iso-8859-1" > > Dear FreeSurfer community, > > I am visually inspecting the quality of my recon -all output for a
large
> dataset and have a rookie question. > > In some instances, when skull stripping ended up leaving some of
the
skull, > these voxels are associated with a "sgmtn label" (cerebral
cortex). In
> other instances, although there are a small number of skull voxels
that
> were not removed automatically, these voxels do not have an
associated
> "sgmnt label" available in TkMedit Tools. > > Is it the case that only the voxels for which there is a
segmentation
label > are actually added to the total grey volume estimate? > > Thus, voxels, which have not been automatically labelled would not
impact
> volume computations? > > Thank you kindly for your help. > -------------- next part -------------- > An HTML attachment was scrubbed... >URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140
1
05/3
92deba7/attachment-0001.html > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: ExCerCor.png > Type: image/png > Size: 81100 bytes > Desc: not available >Url:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/201401
05/
3
92deba7/attachment-0001.png > > ------------------------------ > > Message: 2 > Date: Sun, 5 Jan 2014 15:40:24 -0500 (EST) > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] erroneuos segmentation labeling of skull > outside of brain > To: Yuliya Yoncheva yuliya.yoncheva@gmail.com > Cc: freesurfer@nmr.mgh.harvard.edu > Message-ID:
alpine.LRH.2.03.1401051539450.16518@nmr.mgh.harvard.edu
> Content-Type: text/plain; charset="iso-8859-1" > > Hi Yuliya > > they are included if they are inside of the ?h.pial surface. We
don't
use
> the cortex aseg label as it is in general less accurate than the
surfaces.
> > cheers > Bruce > On Sun, 5 Jan 2014, Yuliya Yoncheva wrote: > > > Dear FreeSurfer community, > > I am visually inspecting the quality of my recon -all output for
a
large
> > dataset and have a rookie question. > > > > In some instances, when skull stripping ended up leaving some of
the
skull, > > these voxels are associated with a "sgmtn label" (cerebral
cortex).
In
other > > instances, although there are a small number of skull voxels
that
were
not > > removed automatically, these voxels do not have an associated
"sgmnt
label" > > available in TkMedit Tools. > > > > Is it the case that only the voxels for which there is a
segmentation
label > > are actually added to the total grey volume estimate?? > > > > Thus, voxels, which have not been automatically labelled would
not
impact > > volume computations? > > > > Thank you kindly for your help. > > > > > > ------------------------------ > > Message: 3 > Date: Sun, 5 Jan 2014 15:55:13 -0500 (EST) > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Motion correction for SPACE FLAIR > To: Octavian Lie octavian.lie@gmail.com > Cc: "freesurfer@nmr.mgh.harvard.edu"
freesurfer@nmr.mgh.harvard.edu
> Message-ID:
alpine.LRH.2.03.1401051554470.16518@nmr.mgh.harvard.edu
> Content-Type: text/plain; charset="windows-1252" > > Hi Octavian > > it's not so easy to reduce the bandwidth in the T2-space
sequences,
but
> certainly you can try. Geometry-matched just means that the FOV
and
> matrix sizes are the same. > > cheers > Bruce > On Fri, 3 Jan 2014, Octavian Lie wrote: > > > Dear Bruce, > > > > Best wishes for 2014! > > > > I will heed your advice and cc to the list. Indeed, the MGH
protocol
I
> > obtained from Andre has one acquisition (NSA). > > Related, I cc this post: > > > > We have been trying adaptations of the T2spaceFLAIR MGH protocol
on
> > our Phillips 3T scanners (sequences called VISTA). Incorporation
of
> > the T2 space FLAIR has been mostly successful at editing out the
dura
> > from the pial surface. The only concern are minute differences > > occasionally appearing as small indentations (at most times
<1-2mm)
> > between the woFLAIR.pial and the final pial surfaces, including
in
> > intrasulcal (duraless) areas; the amount of these small
mismatches
is
> > variable from patient to patients, with some trials with almost > > perfect overlap, and others with visible, if small, differences.
I
> > wonder if this has been your experience too, and if this is due
mostly
> > to bb registration limits or to differences in pixel bandwidth
between
> > mprage and space flair sequences (in our case, see below). > > In FSwiki, the recommendation is that T2 space flair ?should be > > bandwidth, geometry and readout matched to the mprage?. > > > > 1. Speaking about pixel bandwidth, logistics most likely would
not
> > allow application of a MEMPR sequence on our Phillips. According
to
> > Siemens MPRAGE MGH specs, "exceptions indicate that if a
multiple
echo
> > sequence is not available, one should choose a bandwidth of 195 > > Hz/pixel for the MPRAGE". In that case/ using the Siemens Trio
MPRAGE
> > protocol as if the MEMPR is not available, how one would adjust
the
> > bandwidth in T2spaceFLAIR protocol (currently ~650 in the
Siemens
> > space flair and MEMPR protocols) to "match" it to the "simple"
MPRAGE
> > protocol (decreasing it to 195 ?). Would it be a workaround?
(Please
> > comment on the Siemens case, obviously, I do not expect any
light on
> > Phillips without further testing). > > 2. Could you clarify what geometry matched means? > > Please advise, > > > > Thank you, > > > > Octavian > > > > On Fri, Jan 3, 2014 at 9:12 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: > >> Hi Octavian > >> > >> can you cc the list so that others can answer? What is NSA? We
don't
have a > >> ton of experience with it, but 1 has seemed ok (not sure if
we've
ever
tried > >> two) > >> Bruce > >> > >> > >> > >> On Thu, 2 Jan 2014, Octavian Lie wrote: > >> > >>> Dear Bruce, > >>> > >>> Thank you. We used one vs 2 NSA T2 space FLAIR sequences,
without
a
> >>> consistent difference in results, with the 2-NSA run obviously doubling > >>> the > >>> scan time. Is there a preferred number of NSA you recommend,
or we
should > >>> be > >>> fine with one? Both are at resolution 1X1X1 mm. > >>> Thank you, > >>> > >>> Octavian > >>> > >>> > >>> > >>> On Thu, Jan 2, 2014 at 11:56 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu > >>> wrote: > >>> Hi Octaviaan > >>> no, not really. You should motion correct and average them
using
> >>> something like mri_motion_correct* > >>> > >>> We do typically bandwidth/readout match them to the memprages
so
> >>> that there is no differential distortion > >>> > >>> cheers > >>> Bruce > >>> > >>> > >>> On Wed, 1 Jan 2014, Octavian Lie wrote: > >>> > >>> Dear All, > >>> > >>> We recently implemented pial correction using T2 > >>> space FLAIR with freesurfer > >>> v 5.3, mostly successfully. We use 2-3 MPRAGE > >>> (sagittal + axial and/or > >>> coronal) volumes as 001.mgz, 002/003.mgz for the > >>> motion correction step in > >>> recon-all pipeline. > >>> The typical times for acquiring space FLAIR in our > >>> settings vary from 2.5 to > >>> 6 min, depending on the resolution/NSA no. I was > >>> wondering how freesurfer > >>> deals with motion artifacts in the space FLAIR > >>> sequence (especially with > >>> longer acquisition times), and if there is a > >>> strategy to minimize motion > >>> distortion with these (such as getting second runs > >>> for averaging, etc). > >>> Please advise, > >>> > >>> Octavian. > >>> > >>> > >>> > >>> > >>> The information in this e-mail is intended only for the person
to
whom
> >>> it is > >>> addressed. If you believe this e-mail was sent to you in error
and
the
> >>> e-mail > >>> contains patient information, please contact the Partners
Compliance
> >>> HelpLine at > >>> http://www.partners.org/complianceline . If the e-mail was
sent to
you
> >>> in error > >>> but does not contain patient information, please contact the
sender
> >>> and properly > >>> dispose of the e-mail. > >>> > >>> > >>> > >> > > > > > > > > ------------------------------ > > Message: 4 > Date: Sun, 5 Jan 2014 19:25:53 -0500 > From: Yuliya Yoncheva yuliya.yoncheva@gmail.com > Subject: Re: [Freesurfer] erroneuos segmentation labeling of skull > outside of brain > To: Bruce Fischl fischl@nmr.mgh.harvard.edu > Cc: freesurfer@nmr.mgh.harvard.edu > Message-ID: >
CAGE5uFcchoLxBvaf5Lze9z9_QPU4NGa83WFwZ90auZX3-idsFg@mail.gmail.com
> Content-Type: text/plain; charset="iso-8859-1" > > Hello Bruce, > > thank you very much for your fast response and clarifying that
potential
> voxels outside the pial surface do not impact cortical measures. > > Best, > Yuliya > > > > On Sun, Jan 5, 2014 at 3:40 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote: > > > Hi Yuliya > > > > they are included if they are inside of the ?h.pial surface. We
don't
use > > the cortex aseg label as it is in general less accurate than the surfaces. > > > > cheers > > Bruce > > > > On Sun, 5 Jan 2014, Yuliya Yoncheva wrote: > > > > Dear FreeSurfer community, > >> I am visually inspecting the quality of my recon -all output
for a
large > >> dataset and have a rookie question. > >> > >> In some instances, when skull stripping ended up leaving some
of
the
> >> skull, > >> these voxels are associated with a "sgmtn label" (cerebral
cortex).
In
> >> other > >> instances, although there are a small number of skull voxels
that
were
not > >> removed automatically, these voxels do not have an associated
"sgmnt
> >> label" > >> available in TkMedit Tools. > >> > >> Is it the case that only the voxels for which there is a
segmentation
> >> label > >> are actually added to the total grey volume estimate? > >> > >> Thus, voxels, which have not been automatically labelled would
not
impact > >> volume computations? > >> > >> Thank you kindly for your help. > >> > >> > >> > > > > The information in this e-mail is intended only for the person
to
whom
it > > is > > addressed. If you believe this e-mail was sent to you in error
and
the
> > e-mail > > contains patient information, please contact the Partners
Compliance
> > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent
to
you
in > > error > > but does not contain patient information, please contact the
sender
and
> > properly > > dispose of the e-mail. > > > -------------- next part -------------- > An HTML attachment was scrubbed... >URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140
1
05/e
c136ff2/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Sun, 5 Jan 2014 20:29:06 -0500 (EST) > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] erroneuos segmentation labeling of skull > outside of brain > To: Yuliya Yoncheva yuliya.yoncheva@gmail.com > Cc: freesurfer@nmr.mgh.harvard.edu > Message-ID:
alpine.LRH.2.03.1401052028520.16518@nmr.mgh.harvard.edu
> Content-Type: text/plain; charset="iso-8859-1" > > exactly, or measures derived them them like whole-brain volume > > cheers > Bruce > > On Sun, 5 Jan 2014, Yuliya > Yoncheva wrote: > > > Hello Bruce, > > thank you very much for your fast response and clarifying that
potential
> > voxels outside the pial surface do not impact cortical measures. > > > > Best,? > > Yuliya > > > > > > > > On Sun, Jan 5, 2014 at 3:40 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu > > wrote: > > Hi Yuliya > > > > they are included if they are inside of the ?h.pial surface. We > > don't use the cortex aseg label as it is in general less > > accurate than the surfaces. > > > > cheers > > Bruce > > On Sun, 5 Jan 2014, Yuliya Yoncheva wrote: > > > > Dear FreeSurfer community, > > I am visually inspecting the quality of my recon > > -all output for a large > > dataset and have a rookie question. > > > > In some instances, when skull stripping ended up > > leaving some of the skull, > > these voxels are associated with a "sgmtn label" > > (cerebral cortex). In other > > instances, although there are a small number of > > skull voxels that were not > > removed automatically, these voxels do not have an > > associated "sgmnt label" > > available in TkMedit Tools. > > > > Is it the case that only the voxels for which there > > is a segmentation label > > are actually added to the total grey volume > > estimate?? > > > > Thus, voxels, which have not been automatically > > labelled would not impact > > volume computations? > > > > Thank you kindly for your help. > > > > > > > > > > The information in this e-mail is intended only for the person
to
whom
> > it is > > addressed. If you believe this e-mail was sent to you in error
and
the
> > e-mail > > contains patient information, please contact the Partners
Compliance
> > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent
to
you
> > in error > > but does not contain patient information, please contact the
sender
> > and properly > > dispose of the e-mail. > > > > > > > > > > ------------------------------ > > Message: 6 > Date: Sun, 5 Jan 2014 20:50:51 -0500 (EST) > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] recon-all exited w/errors > To: "Boric, Katica A." KBORIC@mgh.harvard.edu > Cc: "freesurfer@nmr.mgh.harvard.edu"
freesurfer@nmr.mgh.harvard.edu
> Message-ID:
alpine.LRH.2.03.1401052049480.16518@nmr.mgh.harvard.edu
> Content-Type: text/plain; charset="iso-8859-1" > > Hi Katica > > what format was the input image to recon-all? Can you verify that
tkmedit
> has the directions correct (that is what it labels as anterior is
actually
> anatomically anterior, etc...). If so, then the talairach just
failed
and
> you will need to either try an alternative (like the MNI or SPM talairachs) > or generate it manually. > > cheers > Bruce > > > > On Thu, 2 Jan 2014, Boric, Katica A. > wrote: > > > Happy New Year freesuerfers! > > I run into this error while doing?recon-all : > > > > ERROR: talairach_afd: Talairach Transform:
transforms/talairach.xfm
> > ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) > > Manual Talairach alignment may be necessary, or > > include the -notal-check flag to skip this test, > > making sure the -notal-check flag follows -all > > or -autorecon1 in the command string. > > > > I would really appreciate if someone could give me some advice
on
how to
fix > > this error. > > > > Thank you very much! > > > > Katica Boric, > > > > > > ps:?Here is the error log: > > > > #@# Talairach Failure Detection Thu Jan ?2 14:20:32 EST 2014 > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > > > ?talairach_afd -T 0.005 -xfm transforms/talairach.xfm? > > > > ERROR: talairach_afd: Talairach Transform:
transforms/talairach.xfm
> > ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) > > INFO: Attempting MINC mritotal to perform Talairach align > > #-------------------------------------------- > > #@# Talairach Thu Jan ?2 14:20:33 EST 2014 > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > > > ?mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50
--no-rescale
--i > > orig.mgz --o orig_nu.mgz? > > > > > > ?talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm? > > > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > /usr/local/freesurfer/bin/talairach > > --i orig_nu.mgz --xfm transforms/talairach.auto.xfm > > $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ > > Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan
8
20:57:42 > > UTC 2013 x86_64 x86_64 x86_64 GNU/Linux > > Thu Jan ?2 14:21:30 EST 2014 > > tmpdir is transforms/tmp.talairach.34005 > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc > > mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc? > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading from orig_nu.mgz... > > TR=8.23, TE=3.22, TI=450.00, flip angle=12.00 > > i_ras = (-1, -9.03383e-08, 0) > > j_ras = (-1.3411e-07, 2.66591e-08, -1) > > k_ras = (1.59256e-07, 1, -5.93718e-09) > > writing to transforms/tmp.talairach.34005/src.mnc... > > -------------------------------------------- > > mritotal -verbose -debug -clobber -modeldir > > /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol
icbm
> > transforms/tmp.talairach.34005/src.mnc
transforms/talairach.auto.xfm
> > Legacy library shellwords.pl will be removed from the Perl core distribution > > in the next major release. Please install it from the CPAN
distribution
> > Perl4::CoreLibs. It is being used at /usr/local/freesurfer/mni/bin/mritotal, > > line 460. > > ? > > ? > > Thu Jan ?2 14:21:43 EST 2014 > > talairach done > > > > ?cp transforms/talairach.auto.xfm transforms/talairach.xfm? > > > > #-------------------------------------------- > > #@# Talairach Failure Detection Thu Jan ?2 14:21:44 EST 2014 > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > > > ?talairach_afd -T 0.005 -xfm transforms/talairach.xfm? > > > > ERROR: talairach_afd: Talairach Transform:
transforms/talairach.xfm
> > ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) > > Manual Talairach alignment may be necessary, or > > include the -notal-check flag to skip this test, > > making sure the -notal-check flag follows -all > > or -autorecon1 in the command string. > > See
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
> > Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan
8
20:57:42 > > UTC 2013 x86_64 x86_64 x86_64 GNU/Linux > > > > recon-all -s xxx_SurferOutput exited with ERRORS at Thu Jan ?2
14:21:45
EST > > 2014 > > > > > > > > > > > > > > ------------------------------ > > Message: 7 > Date: Sun, 5 Jan 2014 23:35:55 -0800 > From: Frank Hsieh two.frank@gmail.com > Subject: [Freesurfer] ROI masks created in FreeSurfer used in
FSL??
> To: freesurfer@nmr.mgh.harvard.edu > Message-ID: >
CABBeRCEt37ZwE1-jHuZGC3Vw-D_v2+svOAnQUcSP6kW37qT4oQ@mail.gmail.com
> Content-Type: text/plain; charset="iso-8859-1" > > Dear FreeSurfer Users, > > I ran recon -all on my structural image and created ROI masks
(using
> mri_label2vol) based on FreeSurfer's cortical parcellation. I'd
like
to
use > these masks for further analysis with FSL. However, it seems that
the
ROI
> masks generated with mri_label2vol have different header
information
than
> that of the original structural image. As a result, I was unable
to
carry
> out further analysis with FSL (e.g., converting these ROI masks
into
> functional space with hires2example_func.mat). I was wondering if
there is
> a way to solve this issue. > > Many thanks in advance. > Frank > -------------- next part -------------- > An HTML attachment was scrubbed... >URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140
1
05/a
552481b/attachment-0001.html > > ------------------------------ > > Message: 8 > Date: Mon, 6 Jan 2014 17:11:54 +0900 > From: Muhammad Naveed Iqbal Qureshi mniqureshi@hotmail.com > Subject: [Freesurfer] converting .thickness files of T1 MRI from > FreeSurfer into AFNI > To: "freesurfer@nmr.mgh.harvard.edu"
freesurfer@nmr.mgh.harvard.edu
> Message-ID: BLU174-W27296B6C59F4D34F89293AC4B70@phx.gbl > Content-Type: text/plain; charset="ks_c_5601-1987" > > Hi, > I want to know that how can I convert FreeSurfer .thickness files
to
AFNI
readable format > I tried the following Command but it gives error > > > mri_convert
/home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness
/media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from
/home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 0, -1) > k_ras = (0, 1, 0) > writing to /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik... > AFNI BRIK write unsupported > ERROR: failure writing /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik > UN:/media> > > Please let me help me to solve this problem > Thank you :) > > > > Best Regards, > > Muhammad > Naveed Iqbal Qureshi > > > -------------- next part -------------- > An HTML attachment was scrubbed... >URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140
1
06/1
d3fe803/attachment-0001.html > > ------------------------------ > > Message: 9 > Date: Mon, 6 Jan 2014 10:45:52 +0100 > From: "L. Schweren" l.j.s.schweren@umcg.nl > Subject: [Freesurfer] brain orientation in qdec > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: 005601cf0ac4$16bda9b0$4438fd10$@umcg.nl > Content-Type: text/plain; charset="us-ascii" > > Dear experts, > > > > I ran recon-all with qcache. When loading the right hemisphere of fsaverage > (or any other surface reconstruction) into tksurfer (for example
command:
> tksurfer fsaverage rh white), the left hemisphere surface is
displayed,
and > it is upside down. When I import annotations they load in the same > orientation as the surface. However, the coordinates and the
labels,
> displayed in the Tksurfer Tools window, are not. For example, when
I
move
> the cursor to the temporal lobe, the label says it's postcentral.
I do
not
> mind manually turning the surfaces in tksurfer, but I do need to
be
sure I
> am looking at the correct hemispheres, coordinates and labels. > > I hope you can help me solve this. Thank you in advance. > > > > Best wishes, > > Lizanne > > > > -------------- next part -------------- > An HTML attachment was scrubbed... >URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140
1
06/5
583e136/attachment-0001.html > > ------------------------------ > > Message: 10 > Date: Mon, 6 Jan 2014 08:41:58 -0500 (EST) > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] converting .thickness files of T1 MRI
from
> FreeSurfer into AFNI > To: Muhammad Naveed Iqbal Qureshi mniqureshi@hotmail.com > Cc: "freesurfer@nmr.mgh.harvard.edu"
freesurfer@nmr.mgh.harvard.edu
> Message-ID:
alpine.LRH.2.03.1401060840550.16518@nmr.mgh.harvard.edu
> Content-Type: text/plain; charset="iso-8859-15" > > Hi Muhammad > > try: > > set sdir=/home/naveed/freesurfer/subjects/CHR01/surf > mris_convert -c $sdir/rh.thickness $sdir/rh.orig
$sdir/rh.thickness.brik
> > cheers > Bruce > > On Mon, 6 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote: > > > Hi, > > I want to know that how can I convert FreeSurfer .thickness
files to
AFNI > > readable format > > I tried the following Command but it gives error > > > > > > mri_convert
/home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness
> > /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading from
/home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness...
> > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > > i_ras = (-1, 0, 0) > > j_ras = (0, 0, -1) > > k_ras = (0, 1, 0) > > writing to /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik... > > AFNI BRIK write unsupported > > ERROR: failure writing > > /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik > > UN:/media> > > > > Please let me help me to solve this problem > > Thank you :)? > > > > Best Regards, > > Muhammad Naveed Iqbal Qureshi > > > > > > ------------------------------ > > Message: 11 > Date: Mon, 6 Jan 2014 10:40:43 -0500 (EST) > From: "Emad Ahmadi" emad@nmr.mgh.harvard.edu > Subject: [Freesurfer] recon-all error > To: freesurfer@nmr.mgh.harvard.edu > Message-ID:
63234.172.19.2.113.1389022843.squirrel@mail.martinos.org
> Content-Type: text/plain; charset="iso-8859-1" > > Hello & Happy New Year! > > I'm running recon-all for one subject on MGH clusters (ERISone),
and
it
> exits with error. I would appreciate it if you help me figure out
what
the
> problem is. The log file is attached. > > All the best throughout 2014! > Emad > > > Emad Ahmadi, MD > ------------------------------------------------ > Research Fellow > Department of Radiology > Massachusetts General Hospital > Harvard Medical School > > 25 New Chardon Street, Suite 400 > Boston, MA 02114 > Tel: 617 726 5237 > Email: emad@nmr.mgh.harvard.edu > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: recon-all.log > Type: application/octet-stream > Size: 20022 bytes > Desc: not available >Url:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/201401
06/
e
6358cca/attachment-0002.obj > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: recon1job.bash > Type: application/octet-stream > Size: 1555 bytes > Desc: not available >Url:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/201401
06/
e
6358cca/attachment-0003.obj > > ------------------------------ > > Message: 12 > Date: Mon, 6 Jan 2014 17:51:18 +0200 > From: Rotem Saar saar.rotem@gmail.com > Subject: [Freesurfer] Fwd: Anatomical segmentation - question > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: >
CAMjFEmbcEwbXMOyxw-kuep6NSzdnk=rYHSEvwPGSbiXkBZKxtA@mail.gmail.com
> Content-Type: text/plain; charset="windows-1252" > > Dear freesurfer experts, > > I'm performing anatomical segmentation for Philips dicoms (3T
scanner). I
> got these two images from the same slice while performing step
number
4 in
> the script below ? from some reason, the two images don't fit.
Should
I
use > "scale brain" ? I know this is not recommended thus want to
consult
with u
> first ? Can u please comment on why this is happening? Is there
any
value
> that corresponds to "how good is the segmentation" ? if yes, where
can
I
> find it ? > > My script is written below. > > Thanks, > > Rotem > > Anatomical segmentation: > > first step- 23 hours: > > *recon-all -autorecon-all -i ~/Desktop/ FOLDER-NAME /I00001.dcm -s > FOLDER-NAME* > > second step:(gyrus=green, sulcus=red) > > *tksurfer -curv FOLDER-NAME lh/rh inflated* > > third step: (talairch registretion) > > *tkmedit FOLDER-NAME brainmask.mgz* > > File-> transforms-> load transform AUX-> Browse-> talairch.xfm > > forth step: (simetry - allows changing 12df transformation. if we
made
any
> changes we should click "save reg" and run this command again) > > *tkregister2 --mgz --s FOLDER-NAME --fstal --surf orig* > > IF WE CHANGE ANYTHING, CLICK "SAVE REG" AND RUN FROM STARTING
POING:
> recon-all -all -subjectid FOLDER-NAME > > fifth step: (scalp removal: if removed too much, rise up from the
value
25: > > *recon-all -skullstrip -wsthresh 25 -clean-bm -no-wsgcaatlas -s > FOLDER-NAME * > > to check the result press: *tkmedit FOLDER-NAME brainmask.mgz
lh.white
-aux > T1.mgz -aux-surface rh.white *) > > for hand correction: *tkmedit FOLDER-NAME brainmask.mgz -aux
T1.mgz*
> > tools-> configure volume brush -> MARK: mode=clone, source=Aux > > tools-> configure brush info (for choosing brush size) > > click on edit voxels: click in MIDDLE for adding voxels, RIGHT for removing > voxels : slice by slice. > > when finish, click: File-> save main volume > > sisxt step: (cp for correcting segmentation) > > *tkmedit FOLDER-NAME brainmask.mgz lh.white -aux T1.mgz
-aux-surface
> rh.white* > > seventh step: (done) > > *recon-all -autorecon2-cp -autorecon3 -s FOLDER-NAME* > > > > > > Rotem Saar-Ashkenazy > Department of Brain and Cognitive Science > Ben Gurion University of the Negev > Beer-Sheva 84105 > Israel > -------------- next part -------------- > An HTML attachment was scrubbed... >URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140
1
06/3
df4f7b3/attachment.html > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: 3.png > Type: image/png > Size: 299694 bytes > Desc: not available >Url:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/201401
06/
3
df4f7b3/attachment.png > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 119, Issue 6 > ******************************************
does mri/orig.mgz exist? On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Now another error UN:~> mri_surf2vol --surfval surf/rh.thickness paint --hemi rh --fillribbon --template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii gdiagno = -1 Using identity matrix for registration mghRead(mri/orig.mgz, -1): could not open file mri_surf2vol ERROR: reading mri/orig.mgz header
Best Regards, Muhammad Naveed Iqbal Qureshi Ph.D. Candidate Bio-Medical Signal & System Analysis Laboratory Department of Medical System Engineering Gwangju Institute of Sciences and Technology 123, Cheomdangwagi-ro, Buk-gu, Gwangju, 500-712, Republic of Korea Tel : +82-62-715-3266 Email : mniqureshi@gist.ac.kr URL : http://bmssa.gist.ac.kr P please don't print this e-mail unless you really need to
Date: Tue, 7 Jan 2014 08:26:56 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
sorry, I wasn't clear. Try:
mri_surf2vol --surfval surf/rh.thickness paint --hemi rh --fillribbon \ --template mri/orig.mgz --volregidentity {$subj} --outvol
{$subj}_rh.ribbon.nii
On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Still the same error UN:~> mri_surf2vol --surfval surf/rh.thickness.paint --hemi rh
--fillribbon
--template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii gdiagno = -1 ERROR: cannot recognize the type of surf/rh.thickness.paint
Best Regards, Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:20:43 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
try adding "paint" after "surf/rh.thickness". The -surfval switch
takes an
optional format parameter after the file name I think
cheers Bruce
On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Hi Bruce, I have tried to convert by using the following commands but still
some
error
occur. UN:~> set subj=/home/naveed/freesurfer/subjects/CHR01/ UN:~> mri_surf2vol --surfval surf/rh.thickness --hemi rh
--fillribbon
--template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii gdiagno = -1 ERROR: cannot recognize the type of surf/rh.thickness
Can you help me. Thank you.
Best Regards, Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:13:45 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
Hi Muhammad
have you looked at the help? It's pretty extensive. If you have
trouble
post again and Doug should be able to guide you
cheers Bruce On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
> Thank you Bruce, > > Please guide me how can I use mri_surf2vol command on
lh/rh.thickness
files
> to get the output as lh/rh.ribbon.nii for AFNI SUMA. > Thank you > > Best Regards, > Muhammad Naveed Iqbal Qureshi > > > From: freesurfer-request@nmr.mgh.harvard.edu > > Subject: Freesurfer Digest, Vol 119, Issue 6 > > To: freesurfer@nmr.mgh.harvard.edu > > Date: Mon, 6 Jan 2014 10:51:33 -0500 > > > > Send Freesurfer mailing list submissions to > > freesurfer@nmr.mgh.harvard.edu > > > > To subscribe or unsubscribe via the World Wide Web, visit > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > or, via email, send a message with subject or body 'help' to > > freesurfer-request@nmr.mgh.harvard.edu > > > > You can reach the person managing the list at > > freesurfer-owner@nmr.mgh.harvard.edu > > > > When replying, please edit your Subject line so it is more
specific
> > than "Re: Contents of Freesurfer digest..." > > > > > > Today's Topics: > > > > 1. erroneuos segmentation labeling of skull outside of brain > > (Yuliya Yoncheva) > > 2. Re: erroneuos segmentation labeling of skull outside of
brain
> > (Bruce Fischl) > > 3. Re: Motion correction for SPACE FLAIR (Bruce Fischl) > > 4. Re: erroneuos segmentation labeling of skull outside of
brain
> > (Yuliya Yoncheva) > > 5. Re: erroneuos segmentation labeling of skull outside of
brain
> > (Bruce Fischl) > > 6. Re: recon-all exited w/errors (Bruce Fischl) > > 7. ROI masks created in FreeSurfer used in FSL?? (Frank Hsieh) > > 8. converting .thickness files of T1 MRI from FreeSurfer into > > AFNI (Muhammad Naveed Iqbal Qureshi) > > 9. brain orientation in qdec (L. Schweren) > > 10. Re: converting .thickness files of T1 MRI from FreeSurfer > > into AFNI (Bruce Fischl) > > 11. recon-all error (Emad Ahmadi) > > 12. Fwd: Anatomical segmentation - question (Rotem Saar) > > > > > >
> > > > Message: 1 > > Date: Sun, 5 Jan 2014 15:14:39 -0500 > > From: Yuliya Yoncheva yuliya.yoncheva@gmail.com > > Subject: [Freesurfer] erroneuos segmentation labeling of skull
outside
> > of brain > > To: freesurfer@nmr.mgh.harvard.edu > > Message-ID: > >
CAGE5uFc2uD9pMefXjRZE0LQP+GcfhHKWeVkHxOGwDzV1=jYrQA@mail.gmail.com
> > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear FreeSurfer community, > > > > I am visually inspecting the quality of my recon -all output
for a
large
> > dataset and have a rookie question. > > > > In some instances, when skull stripping ended up leaving some
of
the
> skull, > > these voxels are associated with a "sgmtn label" (cerebral
cortex). In
> > other instances, although there are a small number of skull
voxels
that
> > were not removed automatically, these voxels do not have an
associated
> > "sgmnt label" available in TkMedit Tools. > > > > Is it the case that only the voxels for which there is a
segmentation
> label > > are actually added to the total grey volume estimate? > > > > Thus, voxels, which have not been automatically labelled would
not
impact
> > volume computations? > > > > Thank you kindly for your help. > >
yes as you can see below:
UN:~/CHR01/mri> ls aparc.a2009s+aseg.mgz orig aparc+aseg.mgz orig.mgz aseg.auto.mgz orig_nu.log aseg.auto_noCCseg.label_intensities.txt orig_nu.mgz aseg.auto_noCCseg.mgz rawavg.mgz aseg.mgz rh.ribbon.mgz brain.finalsurfs.mgz ribbon.mgz brainmask.auto.mgz segment.dat brainmask.mgz T1.mgz brain.mgz talairach.label_intensities.txt ctrl_pts.mgz talairach.log filled.mgz talairach_with_skull_2.log lh.ribbon.mgz talairach_with_skull.log mri_nu_correct.mni.log transforms mri_nu_correct.mni.log.bak wm.asegedit.mgz norm.mgz wm.mgz nu.mgz wmparc.mgz nu_noneck.mgz wm.seg.mgz UN:~/CHR01/mri>
Best Regards,
Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:34:20 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
does mri/orig.mgz exist? On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Now another error
UN:~> mri_surf2vol --surfval surf/rh.thickness paint --hemi rh --fillribbon --template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii gdiagno = -1 Using identity matrix for registration mghRead(mri/orig.mgz, -1): could not open file mri_surf2vol ERROR: reading mri/orig.mgz header
Best Regards, Muhammad Naveed Iqbal Qureshi Ph.D. Candidate Bio-Medical Signal & System Analysis Laboratory Department of Medical System Engineering Gwangju Institute of Sciences and Technology 123, Cheomdangwagi-ro, Buk-gu, Gwangju, 500-712, Republic of Korea Tel : +82-62-715-3266 Email : mniqureshi@gist.ac.kr URL : http://bmssa.gist.ac.kr P please don't print this e-mail unless you really need to
Date: Tue, 7 Jan 2014 08:26:56 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
sorry, I wasn't clear. Try:
mri_surf2vol --surfval surf/rh.thickness paint --hemi rh --fillribbon \ --template mri/orig.mgz --volregidentity {$subj} --outvol
{$subj}_rh.ribbon.nii
On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Still the same error
UN:~> mri_surf2vol --surfval surf/rh.thickness.paint --hemi rh
--fillribbon
--template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii gdiagno = -1 ERROR: cannot recognize the type of surf/rh.thickness.paint
Best Regards, Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:20:43 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
try adding "paint" after "surf/rh.thickness". The -surfval switch
takes an
optional format parameter after the file name I think
cheers Bruce
On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Hi Bruce, I have tried to convert by using the following commands but still
some
error
occur.
UN:~> set subj=/home/naveed/freesurfer/subjects/CHR01/ UN:~> mri_surf2vol --surfval surf/rh.thickness --hemi rh
--fillribbon
--template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii gdiagno = -1 ERROR: cannot recognize the type of surf/rh.thickness
Can you help me. Thank you.
Best Regards, Muhammad Naveed Iqbal Qureshi
> Date: Tue, 7 Jan 2014 08:13:45 -0500 > From: fischl@nmr.mgh.harvard.edu > To: mniqureshi@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6 > > Hi Muhammad > > have you looked at the help? It's pretty extensive. If you have
trouble
> post again and Doug should be able to guide you > > cheers > Bruce > On Tue, 7 Jan 2014, Muhammad > Naveed Iqbal Qureshi wrote: > > > Thank you Bruce, > > > > Please guide me how can I use mri_surf2vol command on
lh/rh.thickness
files > > to get the output as lh/rh.ribbon.nii for AFNI SUMA. > > Thank you > > > > Best Regards, > > Muhammad Naveed Iqbal Qureshi > > > > > From: freesurfer-request@nmr.mgh.harvard.edu > > > Subject: Freesurfer Digest, Vol 119, Issue 6 > > > To: freesurfer@nmr.mgh.harvard.edu > > > Date: Mon, 6 Jan 2014 10:51:33 -0500 > > > > > > Send Freesurfer mailing list submissions to > > > freesurfer@nmr.mgh.harvard.edu > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > or, via email, send a message with subject or body 'help' to > > > freesurfer-request@nmr.mgh.harvard.edu > > > > > > You can reach the person managing the list at > > > freesurfer-owner@nmr.mgh.harvard.edu > > > > > > When replying, please edit your Subject line so it is more
specific
> > > than "Re: Contents of Freesurfer digest..." > > > > > > > > > Today's Topics: > > > > > > 1. erroneuos segmentation labeling of skull outside of brain > > > (Yuliya Yoncheva) > > > 2. Re: erroneuos segmentation labeling of skull outside of
brain
> > > (Bruce Fischl) > > > 3. Re: Motion correction for SPACE FLAIR (Bruce Fischl) > > > 4. Re: erroneuos segmentation labeling of skull outside of
brain
> > > (Yuliya Yoncheva) > > > 5. Re: erroneuos segmentation labeling of skull outside of
brain
> > > (Bruce Fischl) > > > 6. Re: recon-all exited w/errors (Bruce Fischl) > > > 7. ROI masks created in FreeSurfer used in FSL?? (Frank Hsieh) > > > 8. converting .thickness files of T1 MRI from FreeSurfer into > > > AFNI (Muhammad Naveed Iqbal Qureshi) > > > 9. brain orientation in qdec (L. Schweren) > > > 10. Re: converting .thickness files of T1 MRI from FreeSurfer > > > into AFNI (Bruce Fischl) > > > 11. recon-all error (Emad Ahmadi) > > > 12. Fwd: Anatomical segmentation - question (Rotem Saar) > > > > > > > > >
> > > > > > Message: 1 > > > Date: Sun, 5 Jan 2014 15:14:39 -0500 > > > From: Yuliya Yoncheva yuliya.yoncheva@gmail.com > > > Subject: [Freesurfer] erroneuos segmentation labeling of skull
outside
> > > of brain > > > To: freesurfer@nmr.mgh.harvard.edu > > > Message-ID: > > >
CAGE5uFc2uD9pMefXjRZE0LQP+GcfhHKWeVkHxOGwDzV1=jYrQA@mail.gmail.com
> > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Dear FreeSurfer community, > > > > > > I am visually inspecting the quality of my recon -all output
for a
large > > > dataset and have a rookie question. > > > > > > In some instances, when skull stripping ended up leaving some
of
the
> > skull, > > > these voxels are associated with a "sgmtn label" (cerebral
cortex). In
> > > other instances, although there are a small number of skull
voxels
that > > > were not removed automatically, these voxels do not have an
associated
> > > "sgmnt label" available in TkMedit Tools. > > > > > > Is it the case that only the voxels for which there is a
segmentation
> > label > > > are actually added to the total grey volume estimate? > > > > > > Thus, voxels, which have not been automatically labelled would
not
impact > > > volume computations? > > > > > > Thank you kindly for your help. > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... >>>URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/2014
0
1
05/3 > > 92deba7/attachment-0001.html > > > -------------- next part -------------- > > > A non-text attachment was scrubbed... > > > Name: ExCerCor.png > > > Type: image/png > > > Size: 81100 bytes > > > Desc: not available > >>Url:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140
1
05/
3 > > 92deba7/attachment-0001.png > > > > > > ------------------------------ > > > > > > Message: 2 > > > Date: Sun, 5 Jan 2014 15:40:24 -0500 (EST) > > > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] erroneuos segmentation labeling of
skull
> > > outside of brain > > > To: Yuliya Yoncheva yuliya.yoncheva@gmail.com > > > Cc: freesurfer@nmr.mgh.harvard.edu > > > Message-ID:
alpine.LRH.2.03.1401051539450.16518@nmr.mgh.harvard.edu
> > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Hi Yuliya > > > > > > they are included if they are inside of the ?h.pial surface.
We
don't
use > > > the cortex aseg label as it is in general less accurate than
the
surfaces. > > > > > > cheers > > > Bruce > > > On Sun, 5 Jan 2014, Yuliya Yoncheva wrote: > > > > > > > Dear FreeSurfer community, > > > > I am visually inspecting the quality of my recon -all output
for
a
large > > > > dataset and have a rookie question. > > > > > > > > In some instances, when skull stripping ended up leaving
some of
the
> > skull, > > > > these voxels are associated with a "sgmtn label" (cerebral
cortex).
In > > other > > > > instances, although there are a small number of skull voxels
that
were > > not > > > > removed automatically, these voxels do not have an
associated
"sgmnt
> > label" > > > > available in TkMedit Tools. > > > > > > > > Is it the case that only the voxels for which there is a segmentation > > label > > > > are actually added to the total grey volume estimate?? > > > > > > > > Thus, voxels, which have not been automatically labelled
would
not
> > impact > > > > volume computations? > > > > > > > > Thank you kindly for your help. > > > > > > > > > > > > > > ------------------------------ > > > > > > Message: 3 > > > Date: Sun, 5 Jan 2014 15:55:13 -0500 (EST) > > > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] Motion correction for SPACE FLAIR > > > To: Octavian Lie octavian.lie@gmail.com > > > Cc: "freesurfer@nmr.mgh.harvard.edu"
freesurfer@nmr.mgh.harvard.edu
> > > Message-ID:
alpine.LRH.2.03.1401051554470.16518@nmr.mgh.harvard.edu
> > > Content-Type: text/plain; charset="windows-1252" > > > > > > Hi Octavian > > > > > > it's not so easy to reduce the bandwidth in the T2-space
sequences,
but > > > certainly you can try. Geometry-matched just means that the
FOV
and
> > > matrix sizes are the same. > > > > > > cheers > > > Bruce > > > On Fri, 3 Jan 2014, Octavian Lie wrote: > > > > > > > Dear Bruce, > > > > > > > > Best wishes for 2014! > > > > > > > > I will heed your advice and cc to the list. Indeed, the MGH
protocol
I > > > > obtained from Andre has one acquisition (NSA). > > > > Related, I cc this post: > > > > > > > > We have been trying adaptations of the T2spaceFLAIR MGH
protocol
on
> > > > our Phillips 3T scanners (sequences called VISTA).
Incorporation
of
> > > > the T2 space FLAIR has been mostly successful at editing out
the
dura > > > > from the pial surface. The only concern are minute
differences
> > > > occasionally appearing as small indentations (at most times
<1-2mm)
> > > > between the woFLAIR.pial and the final pial surfaces,
including
in
> > > > intrasulcal (duraless) areas; the amount of these small
mismatches
is > > > > variable from patient to patients, with some trials with
almost
> > > > perfect overlap, and others with visible, if small,
differences.
I
> > > > wonder if this has been your experience too, and if this is
due
mostly > > > > to bb registration limits or to differences in pixel
bandwidth
between > > > > mprage and space flair sequences (in our case, see below). > > > > In FSwiki, the recommendation is that T2 space flair ?should
be
> > > > bandwidth, geometry and readout matched to the mprage?. > > > > > > > > 1. Speaking about pixel bandwidth, logistics most likely
would
not
> > > > allow application of a MEMPR sequence on our Phillips.
According
to
> > > > Siemens MPRAGE MGH specs, "exceptions indicate that if a
multiple
echo > > > > sequence is not available, one should choose a bandwidth of
195
> > > > Hz/pixel for the MPRAGE". In that case/ using the Siemens
Trio
MPRAGE > > > > protocol as if the MEMPR is not available, how one would
adjust
the
> > > > bandwidth in T2spaceFLAIR protocol (currently ~650 in the
Siemens
> > > > space flair and MEMPR protocols) to "match" it to the
"simple"
MPRAGE > > > > protocol (decreasing it to 195 ?). Would it be a workaround?
(Please
> > > > comment on the Siemens case, obviously, I do not expect any
light on
> > > > Phillips without further testing). > > > > 2. Could you clarify what geometry matched means? > > > > Please advise, > > > > > > > > Thank you, > > > > > > > > Octavian > > > > > > > > On Fri, Jan 3, 2014 at 9:12 PM, Bruce Fischl > > fischl@nmr.mgh.harvard.edu wrote: > > > >> Hi Octavian > > > >> > > > >> can you cc the list so that others can answer? What is NSA?
We
don't > > have a > > > >> ton of experience with it, but 1 has seemed ok (not sure if
we've
ever > > tried > > > >> two) > > > >> Bruce > > > >> > > > >> > > > >> > > > >> On Thu, 2 Jan 2014, Octavian Lie wrote: > > > >> > > > >>> Dear Bruce, > > > >>> > > > >>> Thank you. We used one vs 2 NSA T2 space FLAIR sequences,
without
a > > > >>> consistent difference in results, with the 2-NSA run
obviously
> > doubling > > > >>> the > > > >>> scan time. Is there a preferred number of NSA you
recommend,
or we
> > should > > > >>> be > > > >>> fine with one? Both are at resolution 1X1X1 mm. > > > >>> Thank you, > > > >>> > > > >>> Octavian > > > >>> > > > >>> > > > >>> > > > >>> On Thu, Jan 2, 2014 at 11:56 AM, Bruce Fischl > > fischl@nmr.mgh.harvard.edu > > > >>> wrote: > > > >>> Hi Octaviaan > > > >>> no, not really. You should motion correct and average them
using
> > > >>> something like mri_motion_correct* > > > >>> > > > >>> We do typically bandwidth/readout match them to the
memprages
so
> > > >>> that there is no differential distortion > > > >>> > > > >>> cheers > > > >>> Bruce > > > >>> > > > >>> > > > >>> On Wed, 1 Jan 2014, Octavian Lie wrote: > > > >>> > > > >>> Dear All, > > > >>> > > > >>> We recently implemented pial correction using T2 > > > >>> space FLAIR with freesurfer > > > >>> v 5.3, mostly successfully. We use 2-3 MPRAGE > > > >>> (sagittal + axial and/or > > > >>> coronal) volumes as 001.mgz, 002/003.mgz for the > > > >>> motion correction step in > > > >>> recon-all pipeline. > > > >>> The typical times for acquiring space FLAIR in our > > > >>> settings vary from 2.5 to > > > >>> 6 min, depending on the resolution/NSA no. I was > > > >>> wondering how freesurfer > > > >>> deals with motion artifacts in the space FLAIR > > > >>> sequence (especially with > > > >>> longer acquisition times), and if there is a > > > >>> strategy to minimize motion > > > >>> distortion with these (such as getting second runs > > > >>> for averaging, etc). > > > >>> Please advise, > > > >>> > > > >>> Octavian. > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> The information in this e-mail is intended only for the
person
to
whom > > > >>> it is > > > >>> addressed. If you believe this e-mail was sent to you in
error
and
the > > > >>> e-mail > > > >>> contains patient information, please contact the Partners Compliance > > > >>> HelpLine at > > > >>> http://www.partners.org/complianceline . If the e-mail was
sent to
you > > > >>> in error > > > >>> but does not contain patient information, please contact
the
sender > > > >>> and properly > > > >>> dispose of the e-mail. > > > >>> > > > >>> > > > >>> > > > >> > > > > > > > > > > > > > > > > > > ------------------------------ > > > > > > Message: 4 > > > Date: Sun, 5 Jan 2014 19:25:53 -0500 > > > From: Yuliya Yoncheva yuliya.yoncheva@gmail.com > > > Subject: Re: [Freesurfer] erroneuos segmentation labeling of
skull
> > > outside of brain > > > To: Bruce Fischl fischl@nmr.mgh.harvard.edu > > > Cc: freesurfer@nmr.mgh.harvard.edu > > > Message-ID: > > >
CAGE5uFcchoLxBvaf5Lze9z9_QPU4NGa83WFwZ90auZX3-idsFg@mail.gmail.com
> > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Hello Bruce, > > > > > > thank you very much for your fast response and clarifying that potential > > > voxels outside the pial surface do not impact cortical
measures.
> > > > > > Best, > > > Yuliya > > > > > > > > > > > > On Sun, Jan 5, 2014 at 3:40 PM, Bruce Fischl > > fischl@nmr.mgh.harvard.eduwrote: > > > > > > > Hi Yuliya > > > > > > > > they are included if they are inside of the ?h.pial surface.
We
don't > > use > > > > the cortex aseg label as it is in general less accurate than
the
> > surfaces. > > > > > > > > cheers > > > > Bruce > > > > > > > > On Sun, 5 Jan 2014, Yuliya Yoncheva wrote: > > > > > > > > Dear FreeSurfer community, > > > >> I am visually inspecting the quality of my recon -all
output
for a
> > large > > > >> dataset and have a rookie question. > > > >> > > > >> In some instances, when skull stripping ended up leaving
some
of
the > > > >> skull, > > > >> these voxels are associated with a "sgmtn label" (cerebral
cortex).
In > > > >> other > > > >> instances, although there are a small number of skull
voxels
that
were > > not > > > >> removed automatically, these voxels do not have an
associated
"sgmnt > > > >> label" > > > >> available in TkMedit Tools. > > > >> > > > >> Is it the case that only the voxels for which there is a segmentation > > > >> label > > > >> are actually added to the total grey volume estimate? > > > >> > > > >> Thus, voxels, which have not been automatically labelled
would
not
> > impact > > > >> volume computations? > > > >> > > > >> Thank you kindly for your help. > > > >> > > > >> > > > >> > > > > > > > > The information in this e-mail is intended only for the
person
to
whom > > it > > > > is > > > > addressed. If you believe this e-mail was sent to you in
error
and
the > > > > e-mail > > > > contains patient information, please contact the Partners
Compliance
> > > > HelpLine at > > > > http://www.partners.org/complianceline . If the e-mail was
sent
to
you > > in > > > > error > > > > but does not contain patient information, please contact the
sender
and > > > > properly > > > > dispose of the e-mail. > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... >>>URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/2014
0
1
05/e > > c136ff2/attachment-0001.html > > > > > > ------------------------------ > > > > > > Message: 5 > > > Date: Sun, 5 Jan 2014 20:29:06 -0500 (EST) > > > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] erroneuos segmentation labeling of
skull
> > > outside of brain > > > To: Yuliya Yoncheva yuliya.yoncheva@gmail.com > > > Cc: freesurfer@nmr.mgh.harvard.edu > > > Message-ID:
alpine.LRH.2.03.1401052028520.16518@nmr.mgh.harvard.edu
> > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > exactly, or measures derived them them like whole-brain volume > > > > > > cheers > > > Bruce > > > > > > On Sun, 5 Jan 2014, Yuliya > > > Yoncheva wrote: > > > > > > > Hello Bruce, > > > > thank you very much for your fast response and clarifying
that
potential > > > > voxels outside the pial surface do not impact cortical
measures.
> > > > > > > > Best,? > > > > Yuliya > > > > > > > > > > > > > > > > On Sun, Jan 5, 2014 at 3:40 PM, Bruce Fischl > > fischl@nmr.mgh.harvard.edu > > > > wrote: > > > > Hi Yuliya > > > > > > > > they are included if they are inside of the ?h.pial surface.
We
> > > > don't use the cortex aseg label as it is in general less > > > > accurate than the surfaces. > > > > > > > > cheers > > > > Bruce > > > > On Sun, 5 Jan 2014, Yuliya Yoncheva wrote: > > > > > > > > Dear FreeSurfer community, > > > > I am visually inspecting the quality of my recon > > > > -all output for a large > > > > dataset and have a rookie question. > > > > > > > > In some instances, when skull stripping ended up > > > > leaving some of the skull, > > > > these voxels are associated with a "sgmtn label" > > > > (cerebral cortex). In other > > > > instances, although there are a small number of > > > > skull voxels that were not > > > > removed automatically, these voxels do not have an > > > > associated "sgmnt label" > > > > available in TkMedit Tools. > > > > > > > > Is it the case that only the voxels for which there > > > > is a segmentation label > > > > are actually added to the total grey volume > > > > estimate?? > > > > > > > > Thus, voxels, which have not been automatically > > > > labelled would not impact > > > > volume computations? > > > > > > > > Thank you kindly for your help. > > > > > > > > > > > > > > > > > > > > The information in this e-mail is intended only for the
person
to
whom > > > > it is > > > > addressed. If you believe this e-mail was sent to you in
error
and
the > > > > e-mail > > > > contains patient information, please contact the Partners
Compliance
> > > > HelpLine at > > > > http://www.partners.org/complianceline . If the e-mail was
sent
to
you > > > > in error > > > > but does not contain patient information, please contact the
sender
> > > > and properly > > > > dispose of the e-mail. > > > > > > > > > > > > > > > > > > > > > > ------------------------------ > > > > > > Message: 6 > > > Date: Sun, 5 Jan 2014 20:50:51 -0500 (EST) > > > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] recon-all exited w/errors > > > To: "Boric, Katica A." KBORIC@mgh.harvard.edu > > > Cc: "freesurfer@nmr.mgh.harvard.edu"
freesurfer@nmr.mgh.harvard.edu
> > > Message-ID:
alpine.LRH.2.03.1401052049480.16518@nmr.mgh.harvard.edu
> > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Hi Katica > > > > > > what format was the input image to recon-all? Can you verify
that
tkmedit > > > has the directions correct (that is what it labels as anterior
is
actually > > > anatomically anterior, etc...). If so, then the talairach just
failed
and > > > you will need to either try an alternative (like the MNI or
SPM
> > talairachs) > > > or generate it manually. > > > > > > cheers > > > Bruce > > > > > > > > > > > > On Thu, 2 Jan 2014, Boric, Katica A. > > > wrote: > > > > > > > Happy New Year freesuerfers! > > > > I run into this error while doing?recon-all : > > > > > > > > ERROR: talairach_afd: Talairach Transform:
transforms/talairach.xfm
> > > > ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) > > > > Manual Talairach alignment may be necessary, or > > > > include the -notal-check flag to skip this test, > > > > making sure the -notal-check flag follows -all > > > > or -autorecon1 in the command string. > > > > > > > > I would really appreciate if someone could give me some
advice
on
how to > > fix > > > > this error. > > > > > > > > Thank you very much! > > > > > > > > Katica Boric, > > > > > > > > > > > > ps:?Here is the error log: > > > > > > > > #@# Talairach Failure Detection Thu Jan ?2 14:20:32 EST 2014 > > > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > > > > > > > ?talairach_afd -T 0.005 -xfm transforms/talairach.xfm? > > > > > > > > ERROR: talairach_afd: Talairach Transform:
transforms/talairach.xfm
> > > > ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) > > > > INFO: Attempting MINC mritotal to perform Talairach align > > > > #-------------------------------------------- > > > > #@# Talairach Thu Jan ?2 14:20:33 EST 2014 > > > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > > > > > > > ?mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale > > --i > > > > orig.mgz --o orig_nu.mgz? > > > > > > > > > > > > ?talairach --i orig_nu.mgz --xfm
transforms/talairach.auto.xfm?
> > > > > > > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > > > /usr/local/freesurfer/bin/talairach > > > > --i orig_nu.mgz --xfm transforms/talairach.auto.xfm > > > > $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ > > > > Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue
Jan
8
> > 20:57:42 > > > > UTC 2013 x86_64 x86_64 x86_64 GNU/Linux > > > > Thu Jan ?2 14:21:30 EST 2014 > > > > tmpdir is transforms/tmp.talairach.34005 > > > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > > > mri_convert orig_nu.mgz
transforms/tmp.talairach.34005/src.mnc
> > > > mri_convert orig_nu.mgz
transforms/tmp.talairach.34005/src.mnc?
> > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter
Exp $
> > > > reading from orig_nu.mgz... > > > > TR=8.23, TE=3.22, TI=450.00, flip angle=12.00 > > > > i_ras = (-1, -9.03383e-08, 0) > > > > j_ras = (-1.3411e-07, 2.66591e-08, -1) > > > > k_ras = (1.59256e-07, 1, -5.93718e-09) > > > > writing to transforms/tmp.talairach.34005/src.mnc... > > > > -------------------------------------------- > > > > mritotal -verbose -debug -clobber -modeldir > > > > /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol
icbm
> > > > transforms/tmp.talairach.34005/src.mnc
transforms/talairach.auto.xfm
> > > > Legacy library shellwords.pl will be removed from the Perl
core
> > distribution > > > > in the next major release. Please install it from the CPAN distribution > > > > Perl4::CoreLibs. It is being used at > > /usr/local/freesurfer/mni/bin/mritotal, > > > > line 460. > > > > ? > > > > ? > > > > Thu Jan ?2 14:21:43 EST 2014 > > > > talairach done > > > > > > > > ?cp transforms/talairach.auto.xfm transforms/talairach.xfm? > > > > > > > > #-------------------------------------------- > > > > #@# Talairach Failure Detection Thu Jan ?2 14:21:44 EST 2014 > > > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > > > > > > > ?talairach_afd -T 0.005 -xfm transforms/talairach.xfm? > > > > > > > > ERROR: talairach_afd: Talairach Transform:
transforms/talairach.xfm
> > > > ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) > > > > Manual Talairach alignment may be necessary, or > > > > include the -notal-check flag to skip this test, > > > > making sure the -notal-check flag follows -all > > > > or -autorecon1 in the command string. > > > > See
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
> > > > Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue
Jan
8
> > 20:57:42 > > > > UTC 2013 x86_64 x86_64 x86_64 GNU/Linux > > > > > > > > recon-all -s xxx_SurferOutput exited with ERRORS at Thu Jan
?2
14:21:45 > > EST > > > > 2014 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------ > > > > > > Message: 7 > > > Date: Sun, 5 Jan 2014 23:35:55 -0800 > > > From: Frank Hsieh two.frank@gmail.com > > > Subject: [Freesurfer] ROI masks created in FreeSurfer used in
FSL??
> > > To: freesurfer@nmr.mgh.harvard.edu > > > Message-ID: > > >
CABBeRCEt37ZwE1-jHuZGC3Vw-D_v2+svOAnQUcSP6kW37qT4oQ@mail.gmail.com
> > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Dear FreeSurfer Users, > > > > > > I ran recon -all on my structural image and created ROI masks
(using
> > > mri_label2vol) based on FreeSurfer's cortical parcellation.
I'd
like
to > > use > > > these masks for further analysis with FSL. However, it seems
that
the
ROI > > > masks generated with mri_label2vol have different header
information
than > > > that of the original structural image. As a result, I was
unable
to
carry > > > out further analysis with FSL (e.g., converting these ROI
masks
into
> > > functional space with hires2example_func.mat). I was wondering
if
there is > > > a way to solve this issue. > > > > > > Many thanks in advance. > > > Frank > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... >>>URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/2014
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1
05/a > > 552481b/attachment-0001.html > > > > > > ------------------------------ > > > > > > Message: 8 > > > Date: Mon, 6 Jan 2014 17:11:54 +0900 > > > From: Muhammad Naveed Iqbal Qureshi mniqureshi@hotmail.com > > > Subject: [Freesurfer] converting .thickness files of T1 MRI
from
> > > FreeSurfer into AFNI > > > To: "freesurfer@nmr.mgh.harvard.edu"
freesurfer@nmr.mgh.harvard.edu
> > > Message-ID: BLU174-W27296B6C59F4D34F89293AC4B70@phx.gbl > > > Content-Type: text/plain; charset="ks_c_5601-1987" > > > > > > Hi, > > > I want to know that how can I convert FreeSurfer .thickness
files
to
AFNI > > readable format > > > I tried the following Command but it gives error > > > > > > > > > mri_convert
/home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness
> > /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp
$
> > > reading from /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness... > > > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > > > i_ras = (-1, 0, 0) > > > j_ras = (0, 0, -1) > > > k_ras = (0, 1, 0) > > > writing to > >
/media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik...
> > > AFNI BRIK write unsupported > > > ERROR: failure writing > > /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik > > > UN:/media> > > > > > > Please let me help me to solve this problem > > > Thank you :) > > > > > > > > > > > > Best Regards, > > > > > > Muhammad > > > Naveed Iqbal Qureshi > > > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... >>>URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/2014
0
1
06/1 > > d3fe803/attachment-0001.html > > > > > > ------------------------------ > > > > > > Message: 9 > > > Date: Mon, 6 Jan 2014 10:45:52 +0100 > > > From: "L. Schweren" l.j.s.schweren@umcg.nl > > > Subject: [Freesurfer] brain orientation in qdec > > > To: freesurfer@nmr.mgh.harvard.edu > > > Message-ID: 005601cf0ac4$16bda9b0$4438fd10$@umcg.nl > > > Content-Type: text/plain; charset="us-ascii" > > > > > > Dear experts, > > > > > > > > > > > > I ran recon-all with qcache. When loading the right hemisphere
of
> > fsaverage > > > (or any other surface reconstruction) into tksurfer (for
example
command: > > > tksurfer fsaverage rh white), the left hemisphere surface is displayed, > > and > > > it is upside down. When I import annotations they load in the
same
> > > orientation as the surface. However, the coordinates and the
labels,
> > > displayed in the Tksurfer Tools window, are not. For example,
when
I
move > > > the cursor to the temporal lobe, the label says it's
postcentral.
I do
not > > > mind manually turning the surfaces in tksurfer, but I do need
to
be
sure I > > > am looking at the correct hemispheres, coordinates and labels. > > > > > > I hope you can help me solve this. Thank you in advance. > > > > > > > > > > > > Best wishes, > > > > > > Lizanne > > > > > > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... >>>URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/2014
0
1
06/5 > > 583e136/attachment-0001.html > > > > > > ------------------------------ > > > > > > Message: 10 > > > Date: Mon, 6 Jan 2014 08:41:58 -0500 (EST) > > > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] converting .thickness files of T1
MRI
from
> > > FreeSurfer into AFNI > > > To: Muhammad Naveed Iqbal Qureshi mniqureshi@hotmail.com > > > Cc: "freesurfer@nmr.mgh.harvard.edu"
freesurfer@nmr.mgh.harvard.edu
> > > Message-ID:
alpine.LRH.2.03.1401060840550.16518@nmr.mgh.harvard.edu
> > > Content-Type: text/plain; charset="iso-8859-15" > > > > > > Hi Muhammad > > > > > > try: > > > > > > set sdir=/home/naveed/freesurfer/subjects/CHR01/surf > > > mris_convert -c $sdir/rh.thickness $sdir/rh.orig $sdir/rh.thickness.brik > > > > > > cheers > > > Bruce > > > > > > On Mon, 6 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote: > > > > > > > Hi, > > > > I want to know that how can I convert FreeSurfer .thickness
files to
> > AFNI > > > > readable format > > > > I tried the following Command but it gives error > > > > > > > > > > > > mri_convert
/home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness
> > > >
/media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik
> > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter
Exp $
> > > > reading from /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness... > > > > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > > > > i_ras = (-1, 0, 0) > > > > j_ras = (0, 0, -1) > > > > k_ras = (0, 1, 0) > > > > writing to > >
/media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik...
> > > > AFNI BRIK write unsupported > > > > ERROR: failure writing > > > >
/media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik
> > > > UN:/media> > > > > > > > > Please let me help me to solve this problem > > > > Thank you :)? > > > > > > > > Best Regards, > > > > Muhammad Naveed Iqbal Qureshi > > > > > > > > > > > > > > ------------------------------ > > > > > > Message: 11 > > > Date: Mon, 6 Jan 2014 10:40:43 -0500 (EST) > > > From: "Emad Ahmadi" emad@nmr.mgh.harvard.edu > > > Subject: [Freesurfer] recon-all error > > > To: freesurfer@nmr.mgh.harvard.edu > > > Message-ID:
63234.172.19.2.113.1389022843.squirrel@mail.martinos.org
> > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Hello & Happy New Year! > > > > > > I'm running recon-all for one subject on MGH clusters
(ERISone),
and
it > > > exits with error. I would appreciate it if you help me figure
out
what
the > > > problem is. The log file is attached. > > > > > > All the best throughout 2014! > > > Emad > > > > > > > > > Emad Ahmadi, MD > > > ------------------------------------------------ > > > Research Fellow > > > Department of Radiology > > > Massachusetts General Hospital > > > Harvard Medical School > > > > > > 25 New Chardon Street, Suite 400 > > > Boston, MA 02114 > > > Tel: 617 726 5237 > > > Email: emad@nmr.mgh.harvard.edu > > > > > > -------------- next part -------------- > > > A non-text attachment was scrubbed... > > > Name: recon-all.log > > > Type: application/octet-stream > > > Size: 20022 bytes > > > Desc: not available > >>Url:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140
1
06/
e > > 6358cca/attachment-0002.obj > > > -------------- next part -------------- > > > A non-text attachment was scrubbed... > > > Name: recon1job.bash > > > Type: application/octet-stream > > > Size: 1555 bytes > > > Desc: not available > >>Url:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140
1
06/
e > > 6358cca/attachment-0003.obj > > > > > > ------------------------------ > > > > > > Message: 12 > > > Date: Mon, 6 Jan 2014 17:51:18 +0200 > > > From: Rotem Saar saar.rotem@gmail.com > > > Subject: [Freesurfer] Fwd: Anatomical segmentation - question > > > To: freesurfer@nmr.mgh.harvard.edu > > > Message-ID: > > >
CAMjFEmbcEwbXMOyxw-kuep6NSzdnk=rYHSEvwPGSbiXkBZKxtA@mail.gmail.com
> > > Content-Type: text/plain; charset="windows-1252" > > > > > > Dear freesurfer experts, > > > > > > I'm performing anatomical segmentation for Philips dicoms (3T scanner). I > > > got these two images from the same slice while performing step
number
4 in > > > the script below ? from some reason, the two images don't fit.
Should
I > > use > > > "scale brain" ? I know this is not recommended thus want to
consult
with u > > > first ? Can u please comment on why this is happening? Is
there
any
value > > > that corresponds to "how good is the segmentation" ? if yes,
where
can
I > > > find it ? > > > > > > My script is written below. > > > > > > Thanks, > > > > > > Rotem > > > > > > Anatomical segmentation: > > > > > > first step- 23 hours: > > > > > > *recon-all -autorecon-all -i ~/Desktop/ FOLDER-NAME
/I00001.dcm -s
> > > FOLDER-NAME* > > > > > > second step:(gyrus=green, sulcus=red) > > > > > > *tksurfer -curv FOLDER-NAME lh/rh inflated* > > > > > > third step: (talairch registretion) > > > > > > *tkmedit FOLDER-NAME brainmask.mgz* > > > > > > File-> transforms-> load transform AUX-> Browse-> talairch.xfm > > > > > > forth step: (simetry - allows changing 12df transformation. if
we
made
any > > > changes we should click "save reg" and run this command again) > > > > > > *tkregister2 --mgz --s FOLDER-NAME --fstal --surf orig* > > > > > > IF WE CHANGE ANYTHING, CLICK "SAVE REG" AND RUN FROM STARTING
POING:
> > > recon-all -all -subjectid FOLDER-NAME > > > > > > fifth step: (scalp removal: if removed too much, rise up from
the
value > > 25: > > > > > > *recon-all -skullstrip -wsthresh 25 -clean-bm -no-wsgcaatlas
-s
> > > FOLDER-NAME * > > > > > > to check the result press: *tkmedit FOLDER-NAME brainmask.mgz
lh.white
> > -aux > > > T1.mgz -aux-surface rh.white *) > > > > > > for hand correction: *tkmedit FOLDER-NAME brainmask.mgz -aux
T1.mgz*
> > > > > > tools-> configure volume brush -> MARK: mode=clone, source=Aux > > > > > > tools-> configure brush info (for choosing brush size) > > > > > > click on edit voxels: click in MIDDLE for adding voxels, RIGHT
for
> > removing > > > voxels : slice by slice. > > > > > > when finish, click: File-> save main volume > > > > > > sisxt step: (cp for correcting segmentation) > > > > > > *tkmedit FOLDER-NAME brainmask.mgz lh.white -aux T1.mgz
-aux-surface
> > > rh.white* > > > > > > seventh step: (done) > > > > > > *recon-all -autorecon2-cp -autorecon3 -s FOLDER-NAME* > > > > > > > > > > > > > > > > > > Rotem Saar-Ashkenazy > > > Department of Brain and Cognitive Science > > > Ben Gurion University of the Negev > > > Beer-Sheva 84105 > > > Israel > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... >>>URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/2014
0
1
06/3 > > df4f7b3/attachment.html > > > -------------- next part -------------- > > > A non-text attachment was scrubbed... > > > Name: 3.png > > > Type: image/png > > > Size: 299694 bytes > > > Desc: not available > >>Url:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140
1
06/
3 > > df4f7b3/attachment.png > > > > > > ------------------------------ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > End of Freesurfer Digest, Vol 119, Issue 6 > > > ****************************************** > > > >
can you run
mri_info mri/orig.mgz On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
yes as you can see below: UN:~/CHR01/mri> ls aparc.a2009s+aseg.mgz orig aparc+aseg.mgz orig.mgz aseg.auto.mgz orig_nu.log aseg.auto_noCCseg.label_intensities.txt orig_nu.mgz aseg.auto_noCCseg.mgz rawavg.mgz aseg.mgz rh.ribbon.mgz brain.finalsurfs.mgz ribbon.mgz brainmask.auto.mgz segment.dat brainmask.mgz T1.mgz brain.mgz talairach.label_intensities.txt ctrl_pts.mgz talairach.log filled.mgz talairach_with_skull_2.log lh.ribbon.mgz talairach_with_skull.log mri_nu_correct.mni.log transforms mri_nu_correct.mni.log.bak wm.asegedit.mgz norm.mgz wm.mgz nu.mgz wmparc.mgz nu_noneck.mgz wm.seg.mgz UN:~/CHR01/mri>
Best Regards, Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:34:20 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
does mri/orig.mgz exist? On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Now another error UN:~> mri_surf2vol --surfval surf/rh.thickness paint --hemi rh
--fillribbon
--template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii gdiagno = -1 Using identity matrix for registration mghRead(mri/orig.mgz, -1): could not open file mri_surf2vol ERROR: reading mri/orig.mgz header
Best Regards, Muhammad Naveed Iqbal Qureshi Ph.D. Candidate Bio-Medical Signal & System Analysis Laboratory Department of Medical System Engineering Gwangju Institute of Sciences and Technology 123, Cheomdangwagi-ro, Buk-gu, Gwangju, 500-712, Republic of Korea Tel : +82-62-715-3266 Email : mniqureshi@gist.ac.kr URL : http://bmssa.gist.ac.kr P please don't print this e-mail unless you really need to
Date: Tue, 7 Jan 2014 08:26:56 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
sorry, I wasn't clear. Try:
mri_surf2vol --surfval surf/rh.thickness paint --hemi rh --fillribbon
\
--template mri/orig.mgz --volregidentity {$subj} --outvol
{$subj}_rh.ribbon.nii
On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Still the same error UN:~> mri_surf2vol --surfval surf/rh.thickness.paint --hemi rh
--fillribbon
--template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii gdiagno = -1 ERROR: cannot recognize the type of surf/rh.thickness.paint
Best Regards, Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:20:43 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
try adding "paint" after "surf/rh.thickness". The -surfval switch
takes an
optional format parameter after the file name I think
cheers Bruce
On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
> Hi Bruce, > I have tried to convert by using the following commands but
still
some
error
> occur. > > UN:~> set subj=/home/naveed/freesurfer/subjects/CHR01/ > UN:~> mri_surf2vol --surfval surf/rh.thickness --hemi rh
--fillribbon
> --template mri/orig.mgz --volregidentity {$subj} --outvol > {$subj}_rh.ribbon.nii > gdiagno = -1 > ERROR: cannot recognize the type of surf/rh.thickness > > Can you help me. > Thank you. > > Best Regards, > Muhammad Naveed Iqbal Qureshi > > > > Date: Tue, 7 Jan 2014 08:13:45 -0500 > > From: fischl@nmr.mgh.harvard.edu > > To: mniqureshi@hotmail.com > > CC: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6 > > > > Hi Muhammad > > > > have you looked at the help? It's pretty extensive. If you
have
trouble
> > post again and Doug should be able to guide you > > > > cheers > > Bruce > > On Tue, 7 Jan 2014, Muhammad > > Naveed Iqbal Qureshi wrote: > > > > > Thank you Bruce, > > > > > > Please guide me how can I use mri_surf2vol command on
lh/rh.thickness
> files > > > to get the output as lh/rh.ribbon.nii for AFNI SUMA. > > > Thank you > > > > > > Best Regards, > > > Muhammad Naveed Iqbal Qureshi > > > > > > > From: freesurfer-request@nmr.mgh.harvard.edu > > > > Subject: Freesurfer Digest, Vol 119, Issue 6 > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > Date: Mon, 6 Jan 2014 10:51:33 -0500 > > > > > > > > Send Freesurfer mailing list submissions to > > > > freesurfer@nmr.mgh.harvard.edu > > > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > or, via email, send a message with subject or body 'help'
to
> > > > freesurfer-request@nmr.mgh.harvard.edu > > > > > > > > You can reach the person managing the list at > > > > freesurfer-owner@nmr.mgh.harvard.edu > > > > > > > > When replying, please edit your Subject line so it is more
specific
> > > > than "Re: Contents of Freesurfer digest..." > > > > > > > > > > > > Today's Topics: > > > > > > > > 1. erroneuos segmentation labeling of skull outside of
brain
> > > > (Yuliya Yoncheva) > > > > 2. Re: erroneuos segmentation labeling of skull outside of
brain
> > > > (Bruce Fischl) > > > > 3. Re: Motion correction for SPACE FLAIR (Bruce Fischl) > > > > 4. Re: erroneuos segmentation labeling of skull outside of
brain
> > > > (Yuliya Yoncheva) > > > > 5. Re: erroneuos segmentation labeling of skull outside of
brain
> > > > (Bruce Fischl) > > > > 6. Re: recon-all exited w/errors (Bruce Fischl) > > > > 7. ROI masks created in FreeSurfer used in FSL?? (Frank
Hsieh)
> > > > 8. converting .thickness files of T1 MRI from FreeSurfer
into
> > > > AFNI (Muhammad Naveed Iqbal Qureshi) > > > > 9. brain orientation in qdec (L. Schweren) > > > > 10. Re: converting .thickness files of T1 MRI from
FreeSurfer
> > > > into AFNI (Bruce Fischl) > > > > 11. recon-all error (Emad Ahmadi) > > > > 12. Fwd: Anatomical segmentation - question (Rotem Saar) > > > > > > > > > > > >
> > > > > > > > Message: 1 > > > > Date: Sun, 5 Jan 2014 15:14:39 -0500 > > > > From: Yuliya Yoncheva yuliya.yoncheva@gmail.com > > > > Subject: [Freesurfer] erroneuos segmentation labeling of
skull
outside
> > > > of brain > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > Message-ID: > > > >
CAGE5uFc2uD9pMefXjRZE0LQP+GcfhHKWeVkHxOGwDzV1=jYrQA@mail.gmail.com
> > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > Dear FreeSurfer community, > > > > > > > > I am visually inspecting the quality of my recon -all
output
for a
> large > > > > dataset and have a rookie question. > > > > > > > > In some instances, when skull stripping ended up leaving
some
of
the
> > > skull, > > > > these voxels are associated with a "sgmtn label" (cerebral
cortex). In
> > > > other instances, although there are a small number of
skull
voxels
> that > > > > were not removed automatically, these voxels do not have
an
associated
> > > > "sgmnt label" available in TkMedit Tools. > > > > > > > > Is it the case that only the voxels for which there is a
segmentation
> > > label > > > > are actually added to the total grey volume estimate? > > > > > > > > Thus, voxels, which have not been automatically labelled
would
not
> impact > > > > volume computations? > > > > > > > > Thank you kindly for your help. > > > >
This is the output :
UN:~/CHR01/mri> mri_info mri/orig.mgz mghRead(mri/orig.mgz, -1): could not open file What did I missed while processing?
Best Regards,
Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:38:36 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
can you run
mri_info mri/orig.mgz On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
yes as you can see below:
UN:~/CHR01/mri> ls aparc.a2009s+aseg.mgz orig aparc+aseg.mgz orig.mgz aseg.auto.mgz orig_nu.log aseg.auto_noCCseg.label_intensities.txt orig_nu.mgz aseg.auto_noCCseg.mgz rawavg.mgz aseg.mgz rh.ribbon.mgz brain.finalsurfs.mgz ribbon.mgz brainmask.auto.mgz segment.dat brainmask.mgz T1.mgz brain.mgz talairach.label_intensities.txt ctrl_pts.mgz talairach.log filled.mgz talairach_with_skull_2.log lh.ribbon.mgz talairach_with_skull.log mri_nu_correct.mni.log transforms mri_nu_correct.mni.log.bak wm.asegedit.mgz norm.mgz wm.mgz nu.mgz wmparc.mgz nu_noneck.mgz wm.seg.mgz UN:~/CHR01/mri>
Best Regards, Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:34:20 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
does mri/orig.mgz exist? On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Now another error
UN:~> mri_surf2vol --surfval surf/rh.thickness paint --hemi rh
--fillribbon
--template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii gdiagno = -1 Using identity matrix for registration mghRead(mri/orig.mgz, -1): could not open file mri_surf2vol ERROR: reading mri/orig.mgz header
Best Regards, Muhammad Naveed Iqbal Qureshi Ph.D. Candidate Bio-Medical Signal & System Analysis Laboratory Department of Medical System Engineering Gwangju Institute of Sciences and Technology 123, Cheomdangwagi-ro, Buk-gu, Gwangju, 500-712, Republic of Korea Tel : +82-62-715-3266 Email : mniqureshi@gist.ac.kr URL : http://bmssa.gist.ac.kr P please don't print this e-mail unless you really need to
Date: Tue, 7 Jan 2014 08:26:56 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
sorry, I wasn't clear. Try:
mri_surf2vol --surfval surf/rh.thickness paint --hemi rh --fillribbon
\
--template mri/orig.mgz --volregidentity {$subj} --outvol
{$subj}_rh.ribbon.nii
On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Still the same error
UN:~> mri_surf2vol --surfval surf/rh.thickness.paint --hemi rh
--fillribbon
--template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii gdiagno = -1 ERROR: cannot recognize the type of surf/rh.thickness.paint
Best Regards, Muhammad Naveed Iqbal Qureshi
> Date: Tue, 7 Jan 2014 08:20:43 -0500 > From: fischl@nmr.mgh.harvard.edu > To: mniqureshi@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6 > > try adding "paint" after "surf/rh.thickness". The -surfval switch
takes an
> optional format parameter after the file name I think > > cheers > Bruce > > On Tue, 7 Jan 2014, Muhammad > Naveed Iqbal Qureshi wrote: > > > Hi Bruce, > > I have tried to convert by using the following commands but
still
some
error > > occur. > > > > UN:~> set subj=/home/naveed/freesurfer/subjects/CHR01/ > > UN:~> mri_surf2vol --surfval surf/rh.thickness --hemi rh
--fillribbon
> > --template mri/orig.mgz --volregidentity {$subj} --outvol > > {$subj}_rh.ribbon.nii > > gdiagno = -1 > > ERROR: cannot recognize the type of surf/rh.thickness > > > > Can you help me. > > Thank you. > > > > Best Regards, > > Muhammad Naveed Iqbal Qureshi > > > > > > > Date: Tue, 7 Jan 2014 08:13:45 -0500 > > > From: fischl@nmr.mgh.harvard.edu > > > To: mniqureshi@hotmail.com > > > CC: freesurfer@nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6 > > > > > > Hi Muhammad > > > > > > have you looked at the help? It's pretty extensive. If you
have
trouble > > > post again and Doug should be able to guide you > > > > > > cheers > > > Bruce > > > On Tue, 7 Jan 2014, Muhammad > > > Naveed Iqbal Qureshi wrote: > > > > > > > Thank you Bruce, > > > > > > > > Please guide me how can I use mri_surf2vol command on lh/rh.thickness > > files > > > > to get the output as lh/rh.ribbon.nii for AFNI SUMA. > > > > Thank you > > > > > > > > Best Regards, > > > > Muhammad Naveed Iqbal Qureshi > > > > > > > > > From: freesurfer-request@nmr.mgh.harvard.edu > > > > > Subject: Freesurfer Digest, Vol 119, Issue 6 > > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > > Date: Mon, 6 Jan 2014 10:51:33 -0500 > > > > > > > > > > Send Freesurfer mailing list submissions to > > > > > freesurfer@nmr.mgh.harvard.edu > > > > > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > > >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > > or, via email, send a message with subject or body 'help'
to
> > > > > freesurfer-request@nmr.mgh.harvard.edu > > > > > > > > > > You can reach the person managing the list at > > > > > freesurfer-owner@nmr.mgh.harvard.edu > > > > > > > > > > When replying, please edit your Subject line so it is more specific > > > > > than "Re: Contents of Freesurfer digest..." > > > > > > > > > > > > > > > Today's Topics: > > > > > > > > > > 1. erroneuos segmentation labeling of skull outside of
brain
> > > > > (Yuliya Yoncheva) > > > > > 2. Re: erroneuos segmentation labeling of skull outside of
brain
> > > > > (Bruce Fischl) > > > > > 3. Re: Motion correction for SPACE FLAIR (Bruce Fischl) > > > > > 4. Re: erroneuos segmentation labeling of skull outside of
brain
> > > > > (Yuliya Yoncheva) > > > > > 5. Re: erroneuos segmentation labeling of skull outside of
brain
> > > > > (Bruce Fischl) > > > > > 6. Re: recon-all exited w/errors (Bruce Fischl) > > > > > 7. ROI masks created in FreeSurfer used in FSL?? (Frank
Hsieh)
> > > > > 8. converting .thickness files of T1 MRI from FreeSurfer
into
> > > > > AFNI (Muhammad Naveed Iqbal Qureshi) > > > > > 9. brain orientation in qdec (L. Schweren) > > > > > 10. Re: converting .thickness files of T1 MRI from
FreeSurfer
> > > > > into AFNI (Bruce Fischl) > > > > > 11. recon-all error (Emad Ahmadi) > > > > > 12. Fwd: Anatomical segmentation - question (Rotem Saar) > > > > > > > > > > > > > > >
> > > > > > > > > > Message: 1 > > > > > Date: Sun, 5 Jan 2014 15:14:39 -0500 > > > > > From: Yuliya Yoncheva yuliya.yoncheva@gmail.com > > > > > Subject: [Freesurfer] erroneuos segmentation labeling of
skull
outside > > > > > of brain > > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > > Message-ID: > > > > > CAGE5uFc2uD9pMefXjRZE0LQP+GcfhHKWeVkHxOGwDzV1=jYrQA@mail.gmail.com > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > > > Dear FreeSurfer community, > > > > > > > > > > I am visually inspecting the quality of my recon -all
output
for a
> > large > > > > > dataset and have a rookie question. > > > > > > > > > > In some instances, when skull stripping ended up leaving
some
of
the > > > > skull, > > > > > these voxels are associated with a "sgmtn label" (cerebral cortex). In > > > > > other instances, although there are a small number of
skull
voxels
> > that > > > > > were not removed automatically, these voxels do not have
an
associated > > > > > "sgmnt label" available in TkMedit Tools. > > > > > > > > > > Is it the case that only the voxels for which there is a segmentation > > > > label > > > > > are actually added to the total grey volume estimate? > > > > > > > > > > Thus, voxels, which have not been automatically labelled
would
not
> > impact > > > > > volume computations? > > > > > > > > > > Thank you kindly for your help. > > > > > -------------- next part -------------- > > > > > An HTML attachment was scrubbed... > >>>>URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/201
4
0
1 > > 05/3 > > > > 92deba7/attachment-0001.html > > > > > -------------- next part -------------- > > > > > A non-text attachment was scrubbed... > > > > > Name: ExCerCor.png > > > > > Type: image/png > > > > > Size: 81100 bytes > > > > > Desc: not available > > >>>Url:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/2014
0
1
05/ > > 3 > > > > 92deba7/attachment-0001.png > > > > > > > > > > ------------------------------ > > > > > > > > > > Message: 2 > > > > > Date: Sun, 5 Jan 2014 15:40:24 -0500 (EST) > > > > > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > > > > > Subject: Re: [Freesurfer] erroneuos segmentation labeling
of
skull
> > > > > outside of brain > > > > > To: Yuliya Yoncheva yuliya.yoncheva@gmail.com > > > > > Cc: freesurfer@nmr.mgh.harvard.edu > > > > > Message-ID: alpine.LRH.2.03.1401051539450.16518@nmr.mgh.harvard.edu > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > > > Hi Yuliya > > > > > > > > > > they are included if they are inside of the ?h.pial
surface.
We
don't > > use > > > > > the cortex aseg label as it is in general less accurate
than
the
> > surfaces. > > > > > > > > > > cheers > > > > > Bruce > > > > > On Sun, 5 Jan 2014, Yuliya Yoncheva wrote: > > > > > > > > > > > Dear FreeSurfer community, > > > > > > I am visually inspecting the quality of my recon -all
output
for
a > > large > > > > > > dataset and have a rookie question. > > > > > > > > > > > > In some instances, when skull stripping ended up leaving
some of
the > > > > skull, > > > > > > these voxels are associated with a "sgmtn label"
(cerebral
cortex). > > In > > > > other > > > > > > instances, although there are a small number of skull
voxels
that > > were > > > > not > > > > > > removed automatically, these voxels do not have an
associated
"sgmnt > > > > label" > > > > > > available in TkMedit Tools. > > > > > > > > > > > > Is it the case that only the voxels for which there is a > > segmentation > > > > label > > > > > > are actually added to the total grey volume estimate?? > > > > > > > > > > > > Thus, voxels, which have not been automatically labelled
would
not > > > > impact > > > > > > volume computations? > > > > > > > > > > > > Thank you kindly for your help. > > > > > > > > > > > > > > > > > > > > > > ------------------------------ > > > > > > > > > > Message: 3 > > > > > Date: Sun, 5 Jan 2014 15:55:13 -0500 (EST) > > > > > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > > > > > Subject: Re: [Freesurfer] Motion correction for SPACE
FLAIR
> > > > > To: Octavian Lie octavian.lie@gmail.com > > > > > Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu > > > > > Message-ID: alpine.LRH.2.03.1401051554470.16518@nmr.mgh.harvard.edu > > > > > Content-Type: text/plain; charset="windows-1252" > > > > > > > > > > Hi Octavian > > > > > > > > > > it's not so easy to reduce the bandwidth in the T2-space sequences, > > but > > > > > certainly you can try. Geometry-matched just means that
the
FOV
and > > > > > matrix sizes are the same. > > > > > > > > > > cheers > > > > > Bruce > > > > > On Fri, 3 Jan 2014, Octavian Lie wrote: > > > > > > > > > > > Dear Bruce, > > > > > > > > > > > > Best wishes for 2014! > > > > > > > > > > > > I will heed your advice and cc to the list. Indeed, the
MGH
protocol > > I > > > > > > obtained from Andre has one acquisition (NSA). > > > > > > Related, I cc this post: > > > > > > > > > > > > We have been trying adaptations of the T2spaceFLAIR MGH
protocol
on > > > > > > our Phillips 3T scanners (sequences called VISTA).
Incorporation
of > > > > > > the T2 space FLAIR has been mostly successful at editing
out
the
> > dura > > > > > > from the pial surface. The only concern are minute
differences
> > > > > > occasionally appearing as small indentations (at most
times
<1-2mm) > > > > > > between the woFLAIR.pial and the final pial surfaces,
including
in > > > > > > intrasulcal (duraless) areas; the amount of these small mismatches > > is > > > > > > variable from patient to patients, with some trials with
almost
> > > > > > perfect overlap, and others with visible, if small,
differences.
I > > > > > > wonder if this has been your experience too, and if this
is
due
> > mostly > > > > > > to bb registration limits or to differences in pixel
bandwidth
> > between > > > > > > mprage and space flair sequences (in our case, see
below).
> > > > > > In FSwiki, the recommendation is that T2 space flair
?should
be
> > > > > > bandwidth, geometry and readout matched to the mprage?. > > > > > > > > > > > > 1. Speaking about pixel bandwidth, logistics most likely
would
not > > > > > > allow application of a MEMPR sequence on our Phillips.
According
to > > > > > > Siemens MPRAGE MGH specs, "exceptions indicate that if a multiple > > echo > > > > > > sequence is not available, one should choose a bandwidth
of
195
> > > > > > Hz/pixel for the MPRAGE". In that case/ using the
Siemens
Trio
> > MPRAGE > > > > > > protocol as if the MEMPR is not available, how one would
adjust
the > > > > > > bandwidth in T2spaceFLAIR protocol (currently ~650 in
the
Siemens > > > > > > space flair and MEMPR protocols) to "match" it to the
"simple"
> > MPRAGE > > > > > > protocol (decreasing it to 195 ?). Would it be a
workaround?
(Please > > > > > > comment on the Siemens case, obviously, I do not expect
any
light on > > > > > > Phillips without further testing). > > > > > > 2. Could you clarify what geometry matched means? > > > > > > Please advise, > > > > > > > > > > > > Thank you, > > > > > > > > > > > > Octavian > > > > > > > > > > > > On Fri, Jan 3, 2014 at 9:12 PM, Bruce Fischl > > > > fischl@nmr.mgh.harvard.edu wrote: > > > > > >> Hi Octavian > > > > > >> > > > > > >> can you cc the list so that others can answer? What is
NSA?
We
> > don't > > > > have a > > > > > >> ton of experience with it, but 1 has seemed ok (not
sure if
we've > > ever > > > > tried > > > > > >> two) > > > > > >> Bruce > > > > > >> > > > > > >> > > > > > >> > > > > > >> On Thu, 2 Jan 2014, Octavian Lie wrote: > > > > > >> > > > > > >>> Dear Bruce, > > > > > >>> > > > > > >>> Thank you. We used one vs 2 NSA T2 space FLAIR
sequences,
without > > a > > > > > >>> consistent difference in results, with the 2-NSA run
obviously
> > > > doubling > > > > > >>> the > > > > > >>> scan time. Is there a preferred number of NSA you
recommend,
or we > > > > should > > > > > >>> be > > > > > >>> fine with one? Both are at resolution 1X1X1 mm. > > > > > >>> Thank you, > > > > > >>> > > > > > >>> Octavian > > > > > >>> > > > > > >>> > > > > > >>> > > > > > >>> On Thu, Jan 2, 2014 at 11:56 AM, Bruce Fischl > > > > fischl@nmr.mgh.harvard.edu > > > > > >>> wrote: > > > > > >>> Hi Octaviaan > > > > > >>> no, not really. You should motion correct and average
them
using > > > > > >>> something like mri_motion_correct* > > > > > >>> > > > > > >>> We do typically bandwidth/readout match them to the
memprages
so > > > > > >>> that there is no differential distortion > > > > > >>> > > > > > >>> cheers > > > > > >>> Bruce > > > > > >>> > > > > > >>> > > > > > >>> On Wed, 1 Jan 2014, Octavian Lie wrote: > > > > > >>> > > > > > >>> Dear All, > > > > > >>> > > > > > >>> We recently implemented pial correction using T2 > > > > > >>> space FLAIR with freesurfer > > > > > >>> v 5.3, mostly successfully. We use 2-3 MPRAGE > > > > > >>> (sagittal + axial and/or > > > > > >>> coronal) volumes as 001.mgz, 002/003.mgz for the > > > > > >>> motion correction step in > > > > > >>> recon-all pipeline. > > > > > >>> The typical times for acquiring space FLAIR in our > > > > > >>> settings vary from 2.5 to > > > > > >>> 6 min, depending on the resolution/NSA no. I was > > > > > >>> wondering how freesurfer > > > > > >>> deals with motion artifacts in the space FLAIR > > > > > >>> sequence (especially with > > > > > >>> longer acquisition times), and if there is a > > > > > >>> strategy to minimize motion > > > > > >>> distortion with these (such as getting second runs > > > > > >>> for averaging, etc). > > > > > >>> Please advise, > > > > > >>> > > > > > >>> Octavian. > > > > > >>> > > > > > >>> > > > > > >>> > > > > > >>> > > > > > >>> The information in this e-mail is intended only for
the
person
to > > whom > > > > > >>> it is > > > > > >>> addressed. If you believe this e-mail was sent to you
in
error
and > > the > > > > > >>> e-mail > > > > > >>> contains patient information, please contact the
Partners
> > Compliance > > > > > >>> HelpLine at > > > > > >>> http://www.partners.org/complianceline . If the e-mail
was
sent to > > you > > > > > >>> in error > > > > > >>> but does not contain patient information, please
contact
the
> > sender > > > > > >>> and properly > > > > > >>> dispose of the e-mail. > > > > > >>> > > > > > >>> > > > > > >>> > > > > > >> > > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------ > > > > > > > > > > Message: 4 > > > > > Date: Sun, 5 Jan 2014 19:25:53 -0500 > > > > > From: Yuliya Yoncheva yuliya.yoncheva@gmail.com > > > > > Subject: Re: [Freesurfer] erroneuos segmentation labeling
of
skull
> > > > > outside of brain > > > > > To: Bruce Fischl fischl@nmr.mgh.harvard.edu > > > > > Cc: freesurfer@nmr.mgh.harvard.edu > > > > > Message-ID: > > > > > CAGE5uFcchoLxBvaf5Lze9z9_QPU4NGa83WFwZ90auZX3-idsFg@mail.gmail.com > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > > > Hello Bruce, > > > > > > > > > > thank you very much for your fast response and clarifying
that
> > potential > > > > > voxels outside the pial surface do not impact cortical
measures.
> > > > > > > > > > Best, > > > > > Yuliya > > > > > > > > > > > > > > > > > > > > On Sun, Jan 5, 2014 at 3:40 PM, Bruce Fischl > > > > fischl@nmr.mgh.harvard.eduwrote: > > > > > > > > > > > Hi Yuliya > > > > > > > > > > > > they are included if they are inside of the ?h.pial
surface.
We
> > don't > > > > use > > > > > > the cortex aseg label as it is in general less accurate
than
the
> > > > surfaces. > > > > > > > > > > > > cheers > > > > > > Bruce > > > > > > > > > > > > On Sun, 5 Jan 2014, Yuliya Yoncheva wrote: > > > > > > > > > > > > Dear FreeSurfer community, > > > > > >> I am visually inspecting the quality of my recon -all
output
for a > > > > large > > > > > >> dataset and have a rookie question. > > > > > >> > > > > > >> In some instances, when skull stripping ended up
leaving
some
of > > the > > > > > >> skull, > > > > > >> these voxels are associated with a "sgmtn label"
(cerebral
cortex). > > In > > > > > >> other > > > > > >> instances, although there are a small number of skull
voxels
that > > were > > > > not > > > > > >> removed automatically, these voxels do not have an
associated
> > "sgmnt > > > > > >> label" > > > > > >> available in TkMedit Tools. > > > > > >> > > > > > >> Is it the case that only the voxels for which there is
a
> > segmentation > > > > > >> label > > > > > >> are actually added to the total grey volume estimate? > > > > > >> > > > > > >> Thus, voxels, which have not been automatically
labelled
would
not > > > > impact > > > > > >> volume computations? > > > > > >> > > > > > >> Thank you kindly for your help. > > > > > >> > > > > > >> > > > > > >> > > > > > > > > > > > > The information in this e-mail is intended only for the
person
to > > whom > > > > it > > > > > > is > > > > > > addressed. If you believe this e-mail was sent to you in
error
and > > the > > > > > > e-mail > > > > > > contains patient information, please contact the
Partners
Compliance > > > > > > HelpLine at > > > > > > http://www.partners.org/complianceline . If the e-mail
was
sent
to > > you > > > > in > > > > > > error > > > > > > but does not contain patient information, please contact
the
sender > > and > > > > > > properly > > > > > > dispose of the e-mail. > > > > > > > > > > > -------------- next part -------------- > > > > > An HTML attachment was scrubbed... > >>>>URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/201
4
0
1 > > 05/e > > > > c136ff2/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > > > Message: 5 > > > > > Date: Sun, 5 Jan 2014 20:29:06 -0500 (EST) > > > > > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > > > > > Subject: Re: [Freesurfer] erroneuos segmentation labeling
of
skull
> > > > > outside of brain > > > > > To: Yuliya Yoncheva yuliya.yoncheva@gmail.com > > > > > Cc: freesurfer@nmr.mgh.harvard.edu > > > > > Message-ID: alpine.LRH.2.03.1401052028520.16518@nmr.mgh.harvard.edu > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > > > exactly, or measures derived them them like whole-brain
volume
> > > > > > > > > > cheers > > > > > Bruce > > > > > > > > > > On Sun, 5 Jan 2014, Yuliya > > > > > Yoncheva wrote: > > > > > > > > > > > Hello Bruce, > > > > > > thank you very much for your fast response and
clarifying
that
> > potential > > > > > > voxels outside the pial surface do not impact cortical
measures.
> > > > > > > > > > > > Best,? > > > > > > Yuliya > > > > > > > > > > > > > > > > > > > > > > > > On Sun, Jan 5, 2014 at 3:40 PM, Bruce Fischl > > > > fischl@nmr.mgh.harvard.edu > > > > > > wrote: > > > > > > Hi Yuliya > > > > > > > > > > > > they are included if they are inside of the ?h.pial
surface.
We
> > > > > > don't use the cortex aseg label as it is in general less > > > > > > accurate than the surfaces. > > > > > > > > > > > > cheers > > > > > > Bruce > > > > > > On Sun, 5 Jan 2014, Yuliya Yoncheva wrote: > > > > > > > > > > > > Dear FreeSurfer community, > > > > > > I am visually inspecting the quality of my recon > > > > > > -all output for a large > > > > > > dataset and have a rookie question. > > > > > > > > > > > > In some instances, when skull stripping ended up > > > > > > leaving some of the skull, > > > > > > these voxels are associated with a "sgmtn label" > > > > > > (cerebral cortex). In other > > > > > > instances, although there are a small number of > > > > > > skull voxels that were not > > > > > > removed automatically, these voxels do not have an > > > > > > associated "sgmnt label" > > > > > > available in TkMedit Tools. > > > > > > > > > > > > Is it the case that only the voxels for which there > > > > > > is a segmentation label > > > > > > are actually added to the total grey volume > > > > > > estimate?? > > > > > > > > > > > > Thus, voxels, which have not been automatically > > > > > > labelled would not impact > > > > > > volume computations? > > > > > > > > > > > > Thank you kindly for your help. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > The information in this e-mail is intended only for the
person
to > > whom > > > > > > it is > > > > > > addressed. If you believe this e-mail was sent to you in
error
and > > the > > > > > > e-mail > > > > > > contains patient information, please contact the
Partners
Compliance > > > > > > HelpLine at > > > > > > http://www.partners.org/complianceline . If the e-mail
was
sent
to > > you > > > > > > in error > > > > > > but does not contain patient information, please contact
the
sender > > > > > > and properly > > > > > > dispose of the e-mail. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------ > > > > > > > > > > Message: 6 > > > > > Date: Sun, 5 Jan 2014 20:50:51 -0500 (EST) > > > > > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > > > > > Subject: Re: [Freesurfer] recon-all exited w/errors > > > > > To: "Boric, Katica A." KBORIC@mgh.harvard.edu > > > > > Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu > > > > > Message-ID: alpine.LRH.2.03.1401052049480.16518@nmr.mgh.harvard.edu > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > > > Hi Katica > > > > > > > > > > what format was the input image to recon-all? Can you
verify
that
> > tkmedit > > > > > has the directions correct (that is what it labels as
anterior
is
> > actually > > > > > anatomically anterior, etc...). If so, then the talairach
just
failed > > and > > > > > you will need to either try an alternative (like the MNI
or
SPM
> > > > talairachs) > > > > > or generate it manually. > > > > > > > > > > cheers > > > > > Bruce > > > > > > > > > > > > > > > > > > > > On Thu, 2 Jan 2014, Boric, Katica A. > > > > > wrote: > > > > > > > > > > > Happy New Year freesuerfers! > > > > > > I run into this error while doing?recon-all : > > > > > > > > > > > > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > > > > > > ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) > > > > > > Manual Talairach alignment may be necessary, or > > > > > > include the -notal-check flag to skip this test, > > > > > > making sure the -notal-check flag follows -all > > > > > > or -autorecon1 in the command string. > > > > > > > > > > > > I would really appreciate if someone could give me some
advice
on > > how to > > > > fix > > > > > > this error. > > > > > > > > > > > > Thank you very much! > > > > > > > > > > > > Katica Boric, > > > > > > > > > > > > > > > > > > ps:?Here is the error log: > > > > > > > > > > > > #@# Talairach Failure Detection Thu Jan ?2 14:20:32 EST
2014
> > > > > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > > > > > > > > > > > ?talairach_afd -T 0.005 -xfm transforms/talairach.xfm? > > > > > > > > > > > > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > > > > > > ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) > > > > > > INFO: Attempting MINC mritotal to perform Talairach
align
> > > > > > #-------------------------------------------- > > > > > > #@# Talairach Thu Jan ?2 14:20:33 EST 2014 > > > > > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > > > > > > > > > > > ?mri_nu_correct.mni --n 1 --proto-iters 1000 --distance
50
> > --no-rescale > > > > --i > > > > > > orig.mgz --o orig_nu.mgz? > > > > > > > > > > > > > > > > > > ?talairach --i orig_nu.mgz --xfm
transforms/talairach.auto.xfm?
> > > > > > > > > > > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > > > > > /usr/local/freesurfer/bin/talairach > > > > > > --i orig_nu.mgz --xfm transforms/talairach.auto.xfm > > > > > > $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ > > > > > > Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP
Tue
Jan
8 > > > > 20:57:42 > > > > > > UTC 2013 x86_64 x86_64 x86_64 GNU/Linux > > > > > > Thu Jan ?2 14:21:30 EST 2014 > > > > > > tmpdir is transforms/tmp.talairach.34005 > > > > > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > > > > > mri_convert orig_nu.mgz
transforms/tmp.talairach.34005/src.mnc
> > > > > > mri_convert orig_nu.mgz
transforms/tmp.talairach.34005/src.mnc?
> > > > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16
mreuter
Exp $
> > > > > > reading from orig_nu.mgz... > > > > > > TR=8.23, TE=3.22, TI=450.00, flip angle=12.00 > > > > > > i_ras = (-1, -9.03383e-08, 0) > > > > > > j_ras = (-1.3411e-07, 2.66591e-08, -1) > > > > > > k_ras = (1.59256e-07, 1, -5.93718e-09) > > > > > > writing to transforms/tmp.talairach.34005/src.mnc... > > > > > > -------------------------------------------- > > > > > > mritotal -verbose -debug -clobber -modeldir > > > > > > /usr/local/freesurfer/mni/bin/../share/mni_autoreg
-protocol
icbm > > > > > > transforms/tmp.talairach.34005/src.mnc transforms/talairach.auto.xfm > > > > > > Legacy library shellwords.pl will be removed from the
Perl
core
> > > > distribution > > > > > > in the next major release. Please install it from the
CPAN
> > distribution > > > > > > Perl4::CoreLibs. It is being used at > > > > /usr/local/freesurfer/mni/bin/mritotal, > > > > > > line 460. > > > > > > ? > > > > > > ? > > > > > > Thu Jan ?2 14:21:43 EST 2014 > > > > > > talairach done > > > > > > > > > > > > ?cp transforms/talairach.auto.xfm
transforms/talairach.xfm?
> > > > > > > > > > > > #-------------------------------------------- > > > > > > #@# Talairach Failure Detection Thu Jan ?2 14:21:44 EST
2014
> > > > > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > > > > > > > > > > > ?talairach_afd -T 0.005 -xfm transforms/talairach.xfm? > > > > > > > > > > > > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > > > > > > ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) > > > > > > Manual Talairach alignment may be necessary, or > > > > > > include the -notal-check flag to skip this test, > > > > > > making sure the -notal-check flag follows -all > > > > > > or -autorecon1 in the command string. > > > > > > See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > > > > > > Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP
Tue
Jan
8 > > > > 20:57:42 > > > > > > UTC 2013 x86_64 x86_64 x86_64 GNU/Linux > > > > > > > > > > > > recon-all -s xxx_SurferOutput exited with ERRORS at Thu
Jan
?2
> > 14:21:45 > > > > EST > > > > > > 2014 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------ > > > > > > > > > > Message: 7 > > > > > Date: Sun, 5 Jan 2014 23:35:55 -0800 > > > > > From: Frank Hsieh two.frank@gmail.com > > > > > Subject: [Freesurfer] ROI masks created in FreeSurfer used
in
FSL?? > > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > > Message-ID: > > > > > CABBeRCEt37ZwE1-jHuZGC3Vw-D_v2+svOAnQUcSP6kW37qT4oQ@mail.gmail.com > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > > > Dear FreeSurfer Users, > > > > > > > > > > I ran recon -all on my structural image and created ROI
masks
(using > > > > > mri_label2vol) based on FreeSurfer's cortical
parcellation.
I'd
like > > to > > > > use > > > > > these masks for further analysis with FSL. However, it
seems
that
the > > ROI > > > > > masks generated with mri_label2vol have different header information > > than > > > > > that of the original structural image. As a result, I was
unable
to > > carry > > > > > out further analysis with FSL (e.g., converting these ROI
masks
into > > > > > functional space with hires2example_func.mat). I was
wondering
if
> > there is > > > > > a way to solve this issue. > > > > > > > > > > Many thanks in advance. > > > > > Frank > > > > > -------------- next part -------------- > > > > > An HTML attachment was scrubbed... > >>>>URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/201
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0
1 > > 05/a > > > > 552481b/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > > > Message: 8 > > > > > Date: Mon, 6 Jan 2014 17:11:54 +0900 > > > > > From: Muhammad Naveed Iqbal Qureshi
> > > > > Subject: [Freesurfer] converting .thickness files of T1
MRI
from
> > > > > FreeSurfer into AFNI > > > > > To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu > > > > > Message-ID: BLU174-W27296B6C59F4D34F89293AC4B70@phx.gbl > > > > > Content-Type: text/plain; charset="ks_c_5601-1987" > > > > > > > > > > Hi, > > > > > I want to know that how can I convert FreeSurfer
.thickness
files
to > > AFNI > > > > readable format > > > > > I tried the following Command but it gives error > > > > > > > > > > > > > > > mri_convert /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness > > > >
/media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik
> > > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter
Exp
$
> > > > > reading from > > /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness... > > > > > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > > > > > i_ras = (-1, 0, 0) > > > > > j_ras = (0, 0, -1) > > > > > k_ras = (0, 1, 0) > > > > > writing to > > > >
/media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik...
> > > > > AFNI BRIK write unsupported > > > > > ERROR: failure writing > > > >
/media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik
> > > > > UN:/media> > > > > > > > > > > Please let me help me to solve this problem > > > > > Thank you :) > > > > > > > > > > > > > > > > > > > > Best Regards, > > > > > > > > > > Muhammad > > > > > Naveed Iqbal Qureshi > > > > > > > > > > > > > > > -------------- next part -------------- > > > > > An HTML attachment was scrubbed... > >>>>URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/201
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0
1 > > 06/1 > > > > d3fe803/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > > > Message: 9 > > > > > Date: Mon, 6 Jan 2014 10:45:52 +0100 > > > > > From: "L. Schweren" l.j.s.schweren@umcg.nl > > > > > Subject: [Freesurfer] brain orientation in qdec > > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > > Message-ID: 005601cf0ac4$16bda9b0$4438fd10$@umcg.nl > > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > Dear experts, > > > > > > > > > > > > > > > > > > > > I ran recon-all with qcache. When loading the right
hemisphere
of
> > > > fsaverage > > > > > (or any other surface reconstruction) into tksurfer (for
example
> > command: > > > > > tksurfer fsaverage rh white), the left hemisphere surface
is
> > displayed, > > > > and > > > > > it is upside down. When I import annotations they load in
the
same
> > > > > orientation as the surface. However, the coordinates and
the
labels, > > > > > displayed in the Tksurfer Tools window, are not. For
example,
when
I > > move > > > > > the cursor to the temporal lobe, the label says it's
postcentral.
I do > > not > > > > > mind manually turning the surfaces in tksurfer, but I do
need
to
be > > sure I > > > > > am looking at the correct hemispheres, coordinates and
labels.
> > > > > > > > > > I hope you can help me solve this. Thank you in advance. > > > > > > > > > > > > > > > > > > > > Best wishes, > > > > > > > > > > Lizanne > > > > > > > > > > > > > > > > > > > > -------------- next part -------------- > > > > > An HTML attachment was scrubbed... > >>>>URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/201
4
0
1 > > 06/5 > > > > 583e136/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > > > Message: 10 > > > > > Date: Mon, 6 Jan 2014 08:41:58 -0500 (EST) > > > > > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > > > > > Subject: Re: [Freesurfer] converting .thickness files of
T1
MRI
from > > > > > FreeSurfer into AFNI > > > > > To: Muhammad Naveed Iqbal Qureshi mniqureshi@hotmail.com > > > > > Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu > > > > > Message-ID: alpine.LRH.2.03.1401060840550.16518@nmr.mgh.harvard.edu > > > > > Content-Type: text/plain; charset="iso-8859-15" > > > > > > > > > > Hi Muhammad > > > > > > > > > > try: > > > > > > > > > > set sdir=/home/naveed/freesurfer/subjects/CHR01/surf > > > > > mris_convert -c $sdir/rh.thickness $sdir/rh.orig > > $sdir/rh.thickness.brik > > > > > > > > > > cheers > > > > > Bruce > > > > > > > > > > On Mon, 6 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote: > > > > > > > > > > > Hi, > > > > > > I want to know that how can I convert FreeSurfer
.thickness
files to > > > > AFNI > > > > > > readable format > > > > > > I tried the following Command but it gives error > > > > > > > > > > > > > > > > > > mri_convert /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness > > > > > >
/media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik
> > > > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16
mreuter
Exp $
> > > > > > reading from > > /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness... > > > > > > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > > > > > > i_ras = (-1, 0, 0) > > > > > > j_ras = (0, 0, -1) > > > > > > k_ras = (0, 1, 0) > > > > > > writing to > > > >
/media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik...
> > > > > > AFNI BRIK write unsupported > > > > > > ERROR: failure writing > > > > > >
/media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik
> > > > > > UN:/media> > > > > > > > > > > > > Please let me help me to solve this problem > > > > > > Thank you :)? > > > > > > > > > > > > Best Regards, > > > > > > Muhammad Naveed Iqbal Qureshi > > > > > > > > > > > > > > > > > > > > > > ------------------------------ > > > > > > > > > > Message: 11 > > > > > Date: Mon, 6 Jan 2014 10:40:43 -0500 (EST) > > > > > From: "Emad Ahmadi" emad@nmr.mgh.harvard.edu > > > > > Subject: [Freesurfer] recon-all error > > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > > Message-ID: 63234.172.19.2.113.1389022843.squirrel@mail.martinos.org > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > > > Hello & Happy New Year! > > > > > > > > > > I'm running recon-all for one subject on MGH clusters
(ERISone),
and > > it > > > > > exits with error. I would appreciate it if you help me
figure
out
what > > the > > > > > problem is. The log file is attached. > > > > > > > > > > All the best throughout 2014! > > > > > Emad > > > > > > > > > > > > > > > Emad Ahmadi, MD > > > > > ------------------------------------------------ > > > > > Research Fellow > > > > > Department of Radiology > > > > > Massachusetts General Hospital > > > > > Harvard Medical School > > > > > > > > > > 25 New Chardon Street, Suite 400 > > > > > Boston, MA 02114 > > > > > Tel: 617 726 5237 > > > > > Email: emad@nmr.mgh.harvard.edu > > > > > > > > > > -------------- next part -------------- > > > > > A non-text attachment was scrubbed... > > > > > Name: recon-all.log > > > > > Type: application/octet-stream > > > > > Size: 20022 bytes > > > > > Desc: not available > > >>>Url:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/2014
0
1
06/ > > e > > > > 6358cca/attachment-0002.obj > > > > > -------------- next part -------------- > > > > > A non-text attachment was scrubbed... > > > > > Name: recon1job.bash > > > > > Type: application/octet-stream > > > > > Size: 1555 bytes > > > > > Desc: not available > > >>>Url:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/2014
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06/ > > e > > > > 6358cca/attachment-0003.obj > > > > > > > > > > ------------------------------ > > > > > > > > > > Message: 12 > > > > > Date: Mon, 6 Jan 2014 17:51:18 +0200 > > > > > From: Rotem Saar saar.rotem@gmail.com > > > > > Subject: [Freesurfer] Fwd: Anatomical segmentation -
question
> > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > > Message-ID: > > > > > CAMjFEmbcEwbXMOyxw-kuep6NSzdnk=rYHSEvwPGSbiXkBZKxtA@mail.gmail.com > > > > > Content-Type: text/plain; charset="windows-1252" > > > > > > > > > > Dear freesurfer experts, > > > > > > > > > > I'm performing anatomical segmentation for Philips dicoms
(3T
> > scanner). I > > > > > got these two images from the same slice while performing
step
number > > 4 in > > > > > the script below ? from some reason, the two images don't
fit.
Should > > I > > > > use > > > > > "scale brain" ? I know this is not recommended thus want
to
consult > > with u > > > > > first ? Can u please comment on why this is happening? Is
there
any > > value > > > > > that corresponds to "how good is the segmentation" ? if
yes,
where
can > > I > > > > > find it ? > > > > > > > > > > My script is written below. > > > > > > > > > > Thanks, > > > > > > > > > > Rotem > > > > > > > > > > Anatomical segmentation: > > > > > > > > > > first step- 23 hours: > > > > > > > > > > *recon-all -autorecon-all -i ~/Desktop/ FOLDER-NAME
/I00001.dcm -s
> > > > > FOLDER-NAME* > > > > > > > > > > second step:(gyrus=green, sulcus=red) > > > > > > > > > > *tksurfer -curv FOLDER-NAME lh/rh inflated* > > > > > > > > > > third step: (talairch registretion) > > > > > > > > > > *tkmedit FOLDER-NAME brainmask.mgz* > > > > > > > > > > File-> transforms-> load transform AUX-> Browse->
talairch.xfm
> > > > > > > > > > forth step: (simetry - allows changing 12df
transformation. if
we
made > > any > > > > > changes we should click "save reg" and run this command
again)
> > > > > > > > > > *tkregister2 --mgz --s FOLDER-NAME --fstal --surf orig* > > > > > > > > > > IF WE CHANGE ANYTHING, CLICK "SAVE REG" AND RUN FROM
STARTING
POING: > > > > > recon-all -all -subjectid FOLDER-NAME > > > > > > > > > > fifth step: (scalp removal: if removed too much, rise up
from
the
> > value > > > > 25: > > > > > > > > > > *recon-all -skullstrip -wsthresh 25 -clean-bm
-no-wsgcaatlas
-s
> > > > > FOLDER-NAME * > > > > > > > > > > to check the result press: *tkmedit FOLDER-NAME
brainmask.mgz
lh.white > > > > -aux > > > > > T1.mgz -aux-surface rh.white *) > > > > > > > > > > for hand correction: *tkmedit FOLDER-NAME brainmask.mgz
-aux
T1.mgz* > > > > > > > > > > tools-> configure volume brush -> MARK: mode=clone,
source=Aux
> > > > > > > > > > tools-> configure brush info (for choosing brush size) > > > > > > > > > > click on edit voxels: click in MIDDLE for adding voxels,
RIGHT
for
> > > > removing > > > > > voxels : slice by slice. > > > > > > > > > > when finish, click: File-> save main volume > > > > > > > > > > sisxt step: (cp for correcting segmentation) > > > > > > > > > > *tkmedit FOLDER-NAME brainmask.mgz lh.white -aux T1.mgz -aux-surface > > > > > rh.white* > > > > > > > > > > seventh step: (done) > > > > > > > > > > *recon-all -autorecon2-cp -autorecon3 -s FOLDER-NAME* > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Rotem Saar-Ashkenazy > > > > > Department of Brain and Cognitive Science > > > > > Ben Gurion University of the Negev > > > > > Beer-Sheva 84105 > > > > > Israel > > > > > -------------- next part -------------- > > > > > An HTML attachment was scrubbed... > >>>>URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/201
4
0
1 > > 06/3 > > > > df4f7b3/attachment.html > > > > > -------------- next part -------------- > > > > > A non-text attachment was scrubbed... > > > > > Name: 3.png > > > > > Type: image/png > > > > > Size: 299694 bytes > > > > > Desc: not available > > >>>Url:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/2014
0
1
06/ > > 3 > > > > df4f7b3/attachment.png > > > > > > > > > > ------------------------------ > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer@nmr.mgh.harvard.edu > > > > >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > > > > > > > End of Freesurfer Digest, Vol 119, Issue 6 > > > > > ****************************************** > > > > > > > > > > > >
something is wrong with that file. Can you check permissions on it and size?
On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
This is the output : UN:~/CHR01/mri> mri_info mri/orig.mgz mghRead(mri/orig.mgz, -1): could not open file
What did I missed while processing?
Best Regards, Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:38:36 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
can you run
mri_info mri/orig.mgz On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
yes as you can see below: UN:~/CHR01/mri> ls aparc.a2009s+aseg.mgz orig aparc+aseg.mgz orig.mgz aseg.auto.mgz orig_nu.log aseg.auto_noCCseg.label_intensities.txt orig_nu.mgz aseg.auto_noCCseg.mgz rawavg.mgz aseg.mgz rh.ribbon.mgz brain.finalsurfs.mgz ribbon.mgz brainmask.auto.mgz segment.dat brainmask.mgz T1.mgz brain.mgz talairach.label_intensities.txt ctrl_pts.mgz talairach.log filled.mgz talairach_with_skull_2.log lh.ribbon.mgz talairach_with_skull.log mri_nu_correct.mni.log transforms mri_nu_correct.mni.log.bak wm.asegedit.mgz norm.mgz wm.mgz nu.mgz wmparc.mgz nu_noneck.mgz wm.seg.mgz UN:~/CHR01/mri>
Best Regards, Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:34:20 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
does mri/orig.mgz exist? On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Now another error UN:~> mri_surf2vol --surfval surf/rh.thickness paint --hemi rh
--fillribbon
--template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii gdiagno = -1 Using identity matrix for registration mghRead(mri/orig.mgz, -1): could not open file mri_surf2vol ERROR: reading mri/orig.mgz header
Best Regards, Muhammad Naveed Iqbal Qureshi Ph.D. Candidate Bio-Medical Signal & System Analysis Laboratory Department of Medical System Engineering Gwangju Institute of Sciences and Technology 123, Cheomdangwagi-ro, Buk-gu, Gwangju, 500-712, Republic of Korea Tel : +82-62-715-3266 Email : mniqureshi@gist.ac.kr URL : http://bmssa.gist.ac.kr P please don't print this e-mail unless you really need to
Date: Tue, 7 Jan 2014 08:26:56 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
sorry, I wasn't clear. Try:
mri_surf2vol --surfval surf/rh.thickness paint --hemi rh
--fillribbon
\
--template mri/orig.mgz --volregidentity {$subj} --outvol
{$subj}_rh.ribbon.nii
On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
> Still the same error > > UN:~> mri_surf2vol --surfval surf/rh.thickness.paint --hemi rh
--fillribbon
> --template mri/orig.mgz --volregidentity {$subj} --outvol > {$subj}_rh.ribbon.nii > gdiagno = -1 > ERROR: cannot recognize the type of surf/rh.thickness.paint > > > Best Regards, > Muhammad Naveed Iqbal Qureshi > > > > Date: Tue, 7 Jan 2014 08:20:43 -0500 > > From: fischl@nmr.mgh.harvard.edu > > To: mniqureshi@hotmail.com > > CC: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6 > > > > try adding "paint" after "surf/rh.thickness". The -surfval
switch
takes an
> > optional format parameter after the file name I think > > > > cheers > > Bruce > > > > On Tue, 7 Jan 2014, Muhammad > > Naveed Iqbal Qureshi wrote: > > > > > Hi Bruce, > > > I have tried to convert by using the following commands but
still
some
> error > > > occur. > > > > > > UN:~> set subj=/home/naveed/freesurfer/subjects/CHR01/ > > > UN:~> mri_surf2vol --surfval surf/rh.thickness --hemi rh
--fillribbon
> > > --template mri/orig.mgz --volregidentity {$subj} --outvol > > > {$subj}_rh.ribbon.nii > > > gdiagno = -1 > > > ERROR: cannot recognize the type of surf/rh.thickness > > > > > > Can you help me. > > > Thank you. > > > > > > Best Regards, > > > Muhammad Naveed Iqbal Qureshi > > > > > > > > > > Date: Tue, 7 Jan 2014 08:13:45 -0500 > > > > From: fischl@nmr.mgh.harvard.edu > > > > To: mniqureshi@hotmail.com > > > > CC: freesurfer@nmr.mgh.harvard.edu > > > > Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119,
Issue 6
> > > > > > > > Hi Muhammad > > > > > > > > have you looked at the help? It's pretty extensive. If you
have
> trouble > > > > post again and Doug should be able to guide you > > > > > > > > cheers > > > > Bruce > > > > On Tue, 7 Jan 2014, Muhammad > > > > Naveed Iqbal Qureshi wrote: > > > > > > > > > Thank you Bruce, > > > > > > > > > > Please guide me how can I use mri_surf2vol command on > lh/rh.thickness > > > files > > > > > to get the output as lh/rh.ribbon.nii for AFNI SUMA. > > > > > Thank you > > > > > > > > > > Best Regards, > > > > > Muhammad Naveed Iqbal Qureshi > > > > > > > > > > > From: freesurfer-request@nmr.mgh.harvard.edu > > > > > > Subject: Freesurfer Digest, Vol 119, Issue 6 > > > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > > > Date: Mon, 6 Jan 2014 10:51:33 -0500 > > > > > > > > > > > > Send Freesurfer mailing list submissions to > > > > > > freesurfer@nmr.mgh.harvard.edu > > > > > > > > > > > > To subscribe or unsubscribe via the World Wide Web,
visit
> > > > > >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > > > or, via email, send a message with subject or body
'help'
to
> > > > > > freesurfer-request@nmr.mgh.harvard.edu > > > > > > > > > > > > You can reach the person managing the list at > > > > > > freesurfer-owner@nmr.mgh.harvard.edu > > > > > > > > > > > > When replying, please edit your Subject line so it is
more
> specific > > > > > > than "Re: Contents of Freesurfer digest..." > > > > > > > > > > > > > > > > > > Today's Topics: > > > > > > > > > > > > 1. erroneuos segmentation labeling of skull outside of
brain
> > > > > > (Yuliya Yoncheva) > > > > > > 2. Re: erroneuos segmentation labeling of skull
outside of
brain
> > > > > > (Bruce Fischl) > > > > > > 3. Re: Motion correction for SPACE FLAIR (Bruce
Fischl)
> > > > > > 4. Re: erroneuos segmentation labeling of skull
outside of
brain
> > > > > > (Yuliya Yoncheva) > > > > > > 5. Re: erroneuos segmentation labeling of skull
outside of
brain
> > > > > > (Bruce Fischl) > > > > > > 6. Re: recon-all exited w/errors (Bruce Fischl) > > > > > > 7. ROI masks created in FreeSurfer used in FSL??
(Frank
Hsieh)
> > > > > > 8. converting .thickness files of T1 MRI from
FreeSurfer
into
> > > > > > AFNI (Muhammad Naveed Iqbal Qureshi) > > > > > > 9. brain orientation in qdec (L. Schweren) > > > > > > 10. Re: converting .thickness files of T1 MRI from
FreeSurfer
> > > > > > into AFNI (Bruce Fischl) > > > > > > 11. recon-all error (Emad Ahmadi) > > > > > > 12. Fwd: Anatomical segmentation - question (Rotem
Saar)
> > > > > > > > > > > > > > > > > > >
> > > > > > > > > > > > Message: 1 > > > > > > Date: Sun, 5 Jan 2014 15:14:39 -0500 > > > > > > From: Yuliya Yoncheva yuliya.yoncheva@gmail.com > > > > > > Subject: [Freesurfer] erroneuos segmentation labeling
of
skull
> outside > > > > > > of brain > > > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > > > Message-ID: > > > > > > >
CAGE5uFc2uD9pMefXjRZE0LQP+GcfhHKWeVkHxOGwDzV1=jYrQA@mail.gmail.com
> > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > > > > > Dear FreeSurfer community, > > > > > > > > > > > > I am visually inspecting the quality of my recon -all
output
for a
> > > large > > > > > > dataset and have a rookie question. > > > > > > > > > > > > In some instances, when skull stripping ended up
leaving
some
of
> the > > > > > skull, > > > > > > these voxels are associated with a "sgmtn label"
(cerebral
> cortex). In > > > > > > other instances, although there are a small number of
skull
voxels
> > > that > > > > > > were not removed automatically, these voxels do not
have
an
> associated > > > > > > "sgmnt label" available in TkMedit Tools. > > > > > > > > > > > > Is it the case that only the voxels for which there is
a
> segmentation > > > > > label > > > > > > are actually added to the total grey volume estimate? > > > > > > > > > > > > Thus, voxels, which have not been automatically
labelled
would
not
> > > impact > > > > > > volume computations? > > > > > > > > > > > > Thank you kindly for your help. > > > > > >
I am sorry i gave the wrong command: following is the result:
UN:~/CHR01> mri_info mri/orig.mgz Volume information for mri/orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 1670.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = 0.0000, c_r = -0.3715 : x_a = 0.0000, y_a = -0.0000, z_a = 1.0000, c_a = 18.5846 : x_s = -0.0000, y_s = -1.0000, z_s = -0.0000, c_s = 6.4364 talairach xfm : mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 -0.0000 0.0000 127.6285 0.0000 -0.0000 1.0000 -109.4154 -0.0000 -1.0000 -0.0000 134.4364 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 0.0000 0.0000 127.6285 0.0000 0.0000 -1.0000 134.4364 0.0000 1.0000 0.0000 109.4154 0.0000 0.0000 0.0000 1.0000
Best Regards,
Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:43:27 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
something is wrong with that file. Can you check permissions on it and size?
On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
This is the output :
UN:~/CHR01/mri> mri_info mri/orig.mgz mghRead(mri/orig.mgz, -1): could not open file
What did I missed while processing?
Best Regards, Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:38:36 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
can you run
mri_info mri/orig.mgz On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
yes as you can see below:
UN:~/CHR01/mri> ls aparc.a2009s+aseg.mgz orig aparc+aseg.mgz orig.mgz aseg.auto.mgz orig_nu.log aseg.auto_noCCseg.label_intensities.txt orig_nu.mgz aseg.auto_noCCseg.mgz rawavg.mgz aseg.mgz rh.ribbon.mgz brain.finalsurfs.mgz ribbon.mgz brainmask.auto.mgz segment.dat brainmask.mgz T1.mgz brain.mgz talairach.label_intensities.txt ctrl_pts.mgz talairach.log filled.mgz talairach_with_skull_2.log lh.ribbon.mgz talairach_with_skull.log mri_nu_correct.mni.log transforms mri_nu_correct.mni.log.bak wm.asegedit.mgz norm.mgz wm.mgz nu.mgz wmparc.mgz nu_noneck.mgz wm.seg.mgz UN:~/CHR01/mri>
Best Regards, Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:34:20 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
does mri/orig.mgz exist? On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Now another error
UN:~> mri_surf2vol --surfval surf/rh.thickness paint --hemi rh
--fillribbon
--template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii gdiagno = -1 Using identity matrix for registration mghRead(mri/orig.mgz, -1): could not open file mri_surf2vol ERROR: reading mri/orig.mgz header
Best Regards, Muhammad Naveed Iqbal Qureshi Ph.D. Candidate Bio-Medical Signal & System Analysis Laboratory Department of Medical System Engineering Gwangju Institute of Sciences and Technology 123, Cheomdangwagi-ro, Buk-gu, Gwangju, 500-712, Republic of Korea Tel : +82-62-715-3266 Email : mniqureshi@gist.ac.kr URL : http://bmssa.gist.ac.kr P please don't print this e-mail unless you really need to
> Date: Tue, 7 Jan 2014 08:26:56 -0500 > From: fischl@nmr.mgh.harvard.edu > To: mniqureshi@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6 > > sorry, I wasn't clear. Try: > > mri_surf2vol --surfval surf/rh.thickness paint --hemi rh
--fillribbon
\
> --template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii > > On > Tue, 7 Jan 2014, Muhammad Naveed Iqbal > Qureshi wrote: > > > Still the same error > > > > UN:~> mri_surf2vol --surfval surf/rh.thickness.paint --hemi rh --fillribbon > > --template mri/orig.mgz --volregidentity {$subj} --outvol > > {$subj}_rh.ribbon.nii > > gdiagno = -1 > > ERROR: cannot recognize the type of surf/rh.thickness.paint > > > > > > Best Regards, > > Muhammad Naveed Iqbal Qureshi > > > > > > > Date: Tue, 7 Jan 2014 08:20:43 -0500 > > > From: fischl@nmr.mgh.harvard.edu > > > To: mniqureshi@hotmail.com > > > CC: freesurfer@nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6 > > > > > > try adding "paint" after "surf/rh.thickness". The -surfval
switch
takes an > > > optional format parameter after the file name I think > > > > > > cheers > > > Bruce > > > > > > On Tue, 7 Jan 2014, Muhammad > > > Naveed Iqbal Qureshi wrote: > > > > > > > Hi Bruce, > > > > I have tried to convert by using the following commands but
still
some > > error > > > > occur. > > > > > > > > UN:~> set subj=/home/naveed/freesurfer/subjects/CHR01/ > > > > UN:~> mri_surf2vol --surfval surf/rh.thickness --hemi rh --fillribbon > > > > --template mri/orig.mgz --volregidentity {$subj} --outvol > > > > {$subj}_rh.ribbon.nii > > > > gdiagno = -1 > > > > ERROR: cannot recognize the type of surf/rh.thickness > > > > > > > > Can you help me. > > > > Thank you. > > > > > > > > Best Regards, > > > > Muhammad Naveed Iqbal Qureshi > > > > > > > > > > > > > Date: Tue, 7 Jan 2014 08:13:45 -0500 > > > > > From: fischl@nmr.mgh.harvard.edu > > > > > To: mniqureshi@hotmail.com > > > > > CC: freesurfer@nmr.mgh.harvard.edu > > > > > Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119,
Issue 6
> > > > > > > > > > Hi Muhammad > > > > > > > > > > have you looked at the help? It's pretty extensive. If you
have
> > trouble > > > > > post again and Doug should be able to guide you > > > > > > > > > > cheers > > > > > Bruce > > > > > On Tue, 7 Jan 2014, Muhammad > > > > > Naveed Iqbal Qureshi wrote: > > > > > > > > > > > Thank you Bruce, > > > > > > > > > > > > Please guide me how can I use mri_surf2vol command on > > lh/rh.thickness > > > > files > > > > > > to get the output as lh/rh.ribbon.nii for AFNI SUMA. > > > > > > Thank you > > > > > > > > > > > > Best Regards, > > > > > > Muhammad Naveed Iqbal Qureshi > > > > > > > > > > > > > From: freesurfer-request@nmr.mgh.harvard.edu > > > > > > > Subject: Freesurfer Digest, Vol 119, Issue 6 > > > > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > > > > Date: Mon, 6 Jan 2014 10:51:33 -0500 > > > > > > > > > > > > > > Send Freesurfer mailing list submissions to > > > > > > > freesurfer@nmr.mgh.harvard.edu > > > > > > > > > > > > > > To subscribe or unsubscribe via the World Wide Web,
visit
> > > > > > >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > > > > or, via email, send a message with subject or body
'help'
to
> > > > > > > freesurfer-request@nmr.mgh.harvard.edu > > > > > > > > > > > > > > You can reach the person managing the list at > > > > > > > freesurfer-owner@nmr.mgh.harvard.edu > > > > > > > > > > > > > > When replying, please edit your Subject line so it is
more
> > specific > > > > > > > than "Re: Contents of Freesurfer digest..." > > > > > > > > > > > > > > > > > > > > > Today's Topics: > > > > > > > > > > > > > > 1. erroneuos segmentation labeling of skull outside of
brain
> > > > > > > (Yuliya Yoncheva) > > > > > > > 2. Re: erroneuos segmentation labeling of skull
outside of
brain > > > > > > > (Bruce Fischl) > > > > > > > 3. Re: Motion correction for SPACE FLAIR (Bruce
Fischl)
> > > > > > > 4. Re: erroneuos segmentation labeling of skull
outside of
brain > > > > > > > (Yuliya Yoncheva) > > > > > > > 5. Re: erroneuos segmentation labeling of skull
outside of
brain > > > > > > > (Bruce Fischl) > > > > > > > 6. Re: recon-all exited w/errors (Bruce Fischl) > > > > > > > 7. ROI masks created in FreeSurfer used in FSL??
(Frank
Hsieh)
> > > > > > > 8. converting .thickness files of T1 MRI from
FreeSurfer
into
> > > > > > > AFNI (Muhammad Naveed Iqbal Qureshi) > > > > > > > 9. brain orientation in qdec (L. Schweren) > > > > > > > 10. Re: converting .thickness files of T1 MRI from
FreeSurfer
> > > > > > > into AFNI (Bruce Fischl) > > > > > > > 11. recon-all error (Emad Ahmadi) > > > > > > > 12. Fwd: Anatomical segmentation - question (Rotem
Saar)
> > > > > > > > > > > > > > > > > > > > > > >
> > > > > > > > > > > > > > Message: 1 > > > > > > > Date: Sun, 5 Jan 2014 15:14:39 -0500 > > > > > > > From: Yuliya Yoncheva yuliya.yoncheva@gmail.com > > > > > > > Subject: [Freesurfer] erroneuos segmentation labeling
of
skull
> > outside > > > > > > > of brain > > > > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > > > > Message-ID: > > > > > > > > >
CAGE5uFc2uD9pMefXjRZE0LQP+GcfhHKWeVkHxOGwDzV1=jYrQA@mail.gmail.com
> > > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > > > > > > > Dear FreeSurfer community, > > > > > > > > > > > > > > I am visually inspecting the quality of my recon -all
output
for a > > > > large > > > > > > > dataset and have a rookie question. > > > > > > > > > > > > > > In some instances, when skull stripping ended up
leaving
some
of > > the > > > > > > skull, > > > > > > > these voxels are associated with a "sgmtn label"
(cerebral
> > cortex). In > > > > > > > other instances, although there are a small number of
skull
voxels > > > > that > > > > > > > were not removed automatically, these voxels do not
have
an
> > associated > > > > > > > "sgmnt label" available in TkMedit Tools. > > > > > > > > > > > > > > Is it the case that only the voxels for which there is
a
> > segmentation > > > > > > label > > > > > > > are actually added to the total grey volume estimate? > > > > > > > > > > > > > > Thus, voxels, which have not been automatically
labelled
would
not > > > > impact > > > > > > > volume computations? > > > > > > > > > > > > > > Thank you kindly for your help. > > > > > > > -------------- next part -------------- > > > > > > > An HTML attachment was scrubbed... > > >>>>>URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20
1
4
0 > > 1 > > > > 05/3 > > > > > > 92deba7/attachment-0001.html > > > > > > > -------------- next part -------------- > > > > > > > A non-text attachment was scrubbed... > > > > > > > Name: ExCerCor.png > > > > > > > Type: image/png > > > > > > > Size: 81100 bytes > > > > > > > Desc: not available > > > >>>>Url:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/201
4
0
1 > > 05/ > > > > 3 > > > > > > 92deba7/attachment-0001.png > > > > > > > > > > > > > > ------------------------------ > > > > > > > > > > > > > > Message: 2 > > > > > > > Date: Sun, 5 Jan 2014 15:40:24 -0500 (EST) > > > > > > > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > > > > > > > Subject: Re: [Freesurfer] erroneuos segmentation
labeling
of
skull > > > > > > > outside of brain > > > > > > > To: Yuliya Yoncheva yuliya.yoncheva@gmail.com > > > > > > > Cc: freesurfer@nmr.mgh.harvard.edu > > > > > > > Message-ID: > > alpine.LRH.2.03.1401051539450.16518@nmr.mgh.harvard.edu > > > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > > > > > > > Hi Yuliya > > > > > > > > > > > > > > they are included if they are inside of the ?h.pial
surface.
We > > don't > > > > use > > > > > > > the cortex aseg label as it is in general less
accurate
than
the > > > > surfaces. > > > > > > > > > > > > > > cheers > > > > > > > Bruce > > > > > > > On Sun, 5 Jan 2014, Yuliya Yoncheva wrote: > > > > > > > > > > > > > > > Dear FreeSurfer community, > > > > > > > > I am visually inspecting the quality of my recon
-all
output
for > > a > > > > large > > > > > > > > dataset and have a rookie question. > > > > > > > > > > > > > > > > In some instances, when skull stripping ended up
leaving
some of > > the > > > > > > skull, > > > > > > > > these voxels are associated with a "sgmtn label"
(cerebral
> > cortex). > > > > In > > > > > > other > > > > > > > > instances, although there are a small number of
skull
voxels
> > that > > > > were > > > > > > not > > > > > > > > removed automatically, these voxels do not have an associated > > "sgmnt > > > > > > label" > > > > > > > > available in TkMedit Tools. > > > > > > > > > > > > > > > > Is it the case that only the voxels for which there
is a
> > > > segmentation > > > > > > label > > > > > > > > are actually added to the total grey volume
estimate??
> > > > > > > > > > > > > > > > Thus, voxels, which have not been automatically
labelled
would > > not > > > > > > impact > > > > > > > > volume computations? > > > > > > > > > > > > > > > > Thank you kindly for your help. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------ > > > > > > > > > > > > > > Message: 3 > > > > > > > Date: Sun, 5 Jan 2014 15:55:13 -0500 (EST) > > > > > > > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > > > > > > > Subject: Re: [Freesurfer] Motion correction for SPACE
FLAIR
> > > > > > > To: Octavian Lie octavian.lie@gmail.com > > > > > > > Cc: "freesurfer@nmr.mgh.harvard.edu" > > freesurfer@nmr.mgh.harvard.edu > > > > > > > Message-ID: > > alpine.LRH.2.03.1401051554470.16518@nmr.mgh.harvard.edu > > > > > > > Content-Type: text/plain; charset="windows-1252" > > > > > > > > > > > > > > Hi Octavian > > > > > > > > > > > > > > it's not so easy to reduce the bandwidth in the
T2-space
> > sequences, > > > > but > > > > > > > certainly you can try. Geometry-matched just means
that
the
FOV > > and > > > > > > > matrix sizes are the same. > > > > > > > > > > > > > > cheers > > > > > > > Bruce > > > > > > > On Fri, 3 Jan 2014, Octavian Lie wrote: > > > > > > > > > > > > > > > Dear Bruce, > > > > > > > > > > > > > > > > Best wishes for 2014! > > > > > > > > > > > > > > > > I will heed your advice and cc to the list. Indeed,
the
MGH
> > protocol > > > > I > > > > > > > > obtained from Andre has one acquisition (NSA). > > > > > > > > Related, I cc this post: > > > > > > > > > > > > > > > > We have been trying adaptations of the T2spaceFLAIR
MGH
protocol > > on > > > > > > > > our Phillips 3T scanners (sequences called VISTA). Incorporation > > of > > > > > > > > the T2 space FLAIR has been mostly successful at
editing
out
the > > > > dura > > > > > > > > from the pial surface. The only concern are minute differences > > > > > > > > occasionally appearing as small indentations (at
most
times
> > <1-2mm) > > > > > > > > between the woFLAIR.pial and the final pial
surfaces,
including > > in > > > > > > > > intrasulcal (duraless) areas; the amount of these
small
> > mismatches > > > > is > > > > > > > > variable from patient to patients, with some trials
with
almost > > > > > > > > perfect overlap, and others with visible, if small, differences. > > I > > > > > > > > wonder if this has been your experience too, and if
this
is
due > > > > mostly > > > > > > > > to bb registration limits or to differences in pixel bandwidth > > > > between > > > > > > > > mprage and space flair sequences (in our case, see
below).
> > > > > > > > In FSwiki, the recommendation is that T2 space flair
?should
be > > > > > > > > bandwidth, geometry and readout matched to the
mprage?.
> > > > > > > > > > > > > > > > 1. Speaking about pixel bandwidth, logistics most
likely
would > > not > > > > > > > > allow application of a MEMPR sequence on our
Phillips.
According > > to > > > > > > > > Siemens MPRAGE MGH specs, "exceptions indicate that
if a
> > multiple > > > > echo > > > > > > > > sequence is not available, one should choose a
bandwidth
of
195 > > > > > > > > Hz/pixel for the MPRAGE". In that case/ using the
Siemens
Trio > > > > MPRAGE > > > > > > > > protocol as if the MEMPR is not available, how one
would
adjust > > the > > > > > > > > bandwidth in T2spaceFLAIR protocol (currently ~650
in
the
> > Siemens > > > > > > > > space flair and MEMPR protocols) to "match" it to
the
"simple" > > > > MPRAGE > > > > > > > > protocol (decreasing it to 195 ?). Would it be a
workaround?
> > (Please > > > > > > > > comment on the Siemens case, obviously, I do not
expect
any
> > light on > > > > > > > > Phillips without further testing). > > > > > > > > 2. Could you clarify what geometry matched means? > > > > > > > > Please advise, > > > > > > > > > > > > > > > > Thank you, > > > > > > > > > > > > > > > > Octavian > > > > > > > > > > > > > > > > On Fri, Jan 3, 2014 at 9:12 PM, Bruce Fischl > > > > > > fischl@nmr.mgh.harvard.edu wrote: > > > > > > > >> Hi Octavian > > > > > > > >> > > > > > > > >> can you cc the list so that others can answer? What
is
NSA?
We > > > > don't > > > > > > have a > > > > > > > >> ton of experience with it, but 1 has seemed ok (not
sure if
> > we've > > > > ever > > > > > > tried > > > > > > > >> two) > > > > > > > >> Bruce > > > > > > > >> > > > > > > > >> > > > > > > > >> > > > > > > > >> On Thu, 2 Jan 2014, Octavian Lie wrote: > > > > > > > >> > > > > > > > >>> Dear Bruce, > > > > > > > >>> > > > > > > > >>> Thank you. We used one vs 2 NSA T2 space FLAIR
sequences,
> > without > > > > a > > > > > > > >>> consistent difference in results, with the 2-NSA
run
obviously > > > > > > doubling > > > > > > > >>> the > > > > > > > >>> scan time. Is there a preferred number of NSA you recommend, > > or we > > > > > > should > > > > > > > >>> be > > > > > > > >>> fine with one? Both are at resolution 1X1X1 mm. > > > > > > > >>> Thank you, > > > > > > > >>> > > > > > > > >>> Octavian > > > > > > > >>> > > > > > > > >>> > > > > > > > >>> > > > > > > > >>> On Thu, Jan 2, 2014 at 11:56 AM, Bruce Fischl > > > > > > fischl@nmr.mgh.harvard.edu > > > > > > > >>> wrote: > > > > > > > >>> Hi Octaviaan > > > > > > > >>> no, not really. You should motion correct and
average
them
> > using > > > > > > > >>> something like mri_motion_correct* > > > > > > > >>> > > > > > > > >>> We do typically bandwidth/readout match them to
the
memprages > > so > > > > > > > >>> that there is no differential distortion > > > > > > > >>> > > > > > > > >>> cheers > > > > > > > >>> Bruce > > > > > > > >>> > > > > > > > >>> > > > > > > > >>> On Wed, 1 Jan 2014, Octavian Lie wrote: > > > > > > > >>> > > > > > > > >>> Dear All, > > > > > > > >>> > > > > > > > >>> We recently implemented pial correction using T2 > > > > > > > >>> space FLAIR with freesurfer > > > > > > > >>> v 5.3, mostly successfully. We use 2-3 MPRAGE > > > > > > > >>> (sagittal + axial and/or > > > > > > > >>> coronal) volumes as 001.mgz, 002/003.mgz for the > > > > > > > >>> motion correction step in > > > > > > > >>> recon-all pipeline. > > > > > > > >>> The typical times for acquiring space FLAIR in our > > > > > > > >>> settings vary from 2.5 to > > > > > > > >>> 6 min, depending on the resolution/NSA no. I was > > > > > > > >>> wondering how freesurfer > > > > > > > >>> deals with motion artifacts in the space FLAIR > > > > > > > >>> sequence (especially with > > > > > > > >>> longer acquisition times), and if there is a > > > > > > > >>> strategy to minimize motion > > > > > > > >>> distortion with these (such as getting second runs > > > > > > > >>> for averaging, etc). > > > > > > > >>> Please advise, > > > > > > > >>> > > > > > > > >>> Octavian. > > > > > > > >>> > > > > > > > >>> > > > > > > > >>> > > > > > > > >>> > > > > > > > >>> The information in this e-mail is intended only
for
the
person > > to > > > > whom > > > > > > > >>> it is > > > > > > > >>> addressed. If you believe this e-mail was sent to
you
in
error > > and > > > > the > > > > > > > >>> e-mail > > > > > > > >>> contains patient information, please contact the
Partners
> > > > Compliance > > > > > > > >>> HelpLine at > > > > > > > >>> http://www.partners.org/complianceline . If the
was
> > sent to > > > > you > > > > > > > >>> in error > > > > > > > >>> but does not contain patient information, please
contact
the > > > > sender > > > > > > > >>> and properly > > > > > > > >>> dispose of the e-mail. > > > > > > > >>> > > > > > > > >>> > > > > > > > >>> > > > > > > > >> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------ > > > > > > > > > > > > > > Message: 4 > > > > > > > Date: Sun, 5 Jan 2014 19:25:53 -0500 > > > > > > > From: Yuliya Yoncheva yuliya.yoncheva@gmail.com > > > > > > > Subject: Re: [Freesurfer] erroneuos segmentation
labeling
of
skull > > > > > > > outside of brain > > > > > > > To: Bruce Fischl fischl@nmr.mgh.harvard.edu > > > > > > > Cc: freesurfer@nmr.mgh.harvard.edu > > > > > > > Message-ID: > > > > > > > > >
CAGE5uFcchoLxBvaf5Lze9z9_QPU4NGa83WFwZ90auZX3-idsFg@mail.gmail.com
> > > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > > > > > > > Hello Bruce, > > > > > > > > > > > > > > thank you very much for your fast response and
clarifying
that
> > > > potential > > > > > > > voxels outside the pial surface do not impact cortical measures. > > > > > > > > > > > > > > Best, > > > > > > > Yuliya > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Sun, Jan 5, 2014 at 3:40 PM, Bruce Fischl > > > > > > fischl@nmr.mgh.harvard.eduwrote: > > > > > > > > > > > > > > > Hi Yuliya > > > > > > > > > > > > > > > > they are included if they are inside of the ?h.pial
surface.
We > > > > don't > > > > > > use > > > > > > > > the cortex aseg label as it is in general less
accurate
than
the > > > > > > surfaces. > > > > > > > > > > > > > > > > cheers > > > > > > > > Bruce > > > > > > > > > > > > > > > > On Sun, 5 Jan 2014, Yuliya Yoncheva wrote: > > > > > > > > > > > > > > > > Dear FreeSurfer community, > > > > > > > >> I am visually inspecting the quality of my recon
-all
output > > for a > > > > > > large > > > > > > > >> dataset and have a rookie question. > > > > > > > >> > > > > > > > >> In some instances, when skull stripping ended up
leaving
some > > of > > > > the > > > > > > > >> skull, > > > > > > > >> these voxels are associated with a "sgmtn label"
(cerebral
> > cortex). > > > > In > > > > > > > >> other > > > > > > > >> instances, although there are a small number of
skull
voxels > > that > > > > were > > > > > > not > > > > > > > >> removed automatically, these voxels do not have an associated > > > > "sgmnt > > > > > > > >> label" > > > > > > > >> available in TkMedit Tools. > > > > > > > >> > > > > > > > >> Is it the case that only the voxels for which there
is
a
> > > > segmentation > > > > > > > >> label > > > > > > > >> are actually added to the total grey volume
estimate?
> > > > > > > >> > > > > > > > >> Thus, voxels, which have not been automatically
labelled
would > > not > > > > > > impact > > > > > > > >> volume computations? > > > > > > > >> > > > > > > > >> Thank you kindly for your help. > > > > > > > >> > > > > > > > >> > > > > > > > >> > > > > > > > > > > > > > > > > The information in this e-mail is intended only for
the
person > > to > > > > whom > > > > > > it > > > > > > > > is > > > > > > > > addressed. If you believe this e-mail was sent to
you in
error > > and > > > > the > > > > > > > > e-mail > > > > > > > > contains patient information, please contact the
Partners
> > Compliance > > > > > > > > HelpLine at > > > > > > > > http://www.partners.org/complianceline . If the
was
sent > > to > > > > you > > > > > > in > > > > > > > > error > > > > > > > > but does not contain patient information, please
contact
the
> > sender > > > > and > > > > > > > > properly > > > > > > > > dispose of the e-mail. > > > > > > > > > > > > > > > -------------- next part -------------- > > > > > > > An HTML attachment was scrubbed... > > >>>>>URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20
1
4
0 > > 1 > > > > 05/e > > > > > > c136ff2/attachment-0001.html > > > > > > > > > > > > > > ------------------------------ > > > > > > > > > > > > > > Message: 5 > > > > > > > Date: Sun, 5 Jan 2014 20:29:06 -0500 (EST) > > > > > > > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > > > > > > > Subject: Re: [Freesurfer] erroneuos segmentation
labeling
of
skull > > > > > > > outside of brain > > > > > > > To: Yuliya Yoncheva yuliya.yoncheva@gmail.com > > > > > > > Cc: freesurfer@nmr.mgh.harvard.edu > > > > > > > Message-ID: > > alpine.LRH.2.03.1401052028520.16518@nmr.mgh.harvard.edu > > > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > > > > > > > exactly, or measures derived them them like
whole-brain
volume
> > > > > > > > > > > > > > cheers > > > > > > > Bruce > > > > > > > > > > > > > > On Sun, 5 Jan 2014, Yuliya > > > > > > > Yoncheva wrote: > > > > > > > > > > > > > > > Hello Bruce, > > > > > > > > thank you very much for your fast response and
clarifying
that > > > > potential > > > > > > > > voxels outside the pial surface do not impact
cortical
measures. > > > > > > > > > > > > > > > > Best,? > > > > > > > > Yuliya > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Sun, Jan 5, 2014 at 3:40 PM, Bruce Fischl > > > > > > fischl@nmr.mgh.harvard.edu > > > > > > > > wrote: > > > > > > > > Hi Yuliya > > > > > > > > > > > > > > > > they are included if they are inside of the ?h.pial
surface.
We > > > > > > > > don't use the cortex aseg label as it is in general
less
> > > > > > > > accurate than the surfaces. > > > > > > > > > > > > > > > > cheers > > > > > > > > Bruce > > > > > > > > On Sun, 5 Jan 2014, Yuliya Yoncheva wrote: > > > > > > > > > > > > > > > > Dear FreeSurfer community, > > > > > > > > I am visually inspecting the quality of my recon > > > > > > > > -all output for a large > > > > > > > > dataset and have a rookie question. > > > > > > > > > > > > > > > > In some instances, when skull stripping ended up > > > > > > > > leaving some of the skull, > > > > > > > > these voxels are associated with a "sgmtn label" > > > > > > > > (cerebral cortex). In other > > > > > > > > instances, although there are a small number of > > > > > > > > skull voxels that were not > > > > > > > > removed automatically, these voxels do not have an > > > > > > > > associated "sgmnt label" > > > > > > > > available in TkMedit Tools. > > > > > > > > > > > > > > > > Is it the case that only the voxels for which there > > > > > > > > is a segmentation label > > > > > > > > are actually added to the total grey volume > > > > > > > > estimate?? > > > > > > > > > > > > > > > > Thus, voxels, which have not been automatically > > > > > > > > labelled would not impact > > > > > > > > volume computations? > > > > > > > > > > > > > > > > Thank you kindly for your help. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > The information in this e-mail is intended only for
the
person > > to > > > > whom > > > > > > > > it is > > > > > > > > addressed. If you believe this e-mail was sent to
you in
error > > and > > > > the > > > > > > > > e-mail > > > > > > > > contains patient information, please contact the
Partners
> > Compliance > > > > > > > > HelpLine at > > > > > > > > http://www.partners.org/complianceline . If the
was
sent > > to > > > > you > > > > > > > > in error > > > > > > > > but does not contain patient information, please
contact
the
> > sender > > > > > > > > and properly > > > > > > > > dispose of the e-mail. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------ > > > > > > > > > > > > > > Message: 6 > > > > > > > Date: Sun, 5 Jan 2014 20:50:51 -0500 (EST) > > > > > > > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > > > > > > > Subject: Re: [Freesurfer] recon-all exited w/errors > > > > > > > To: "Boric, Katica A." KBORIC@mgh.harvard.edu > > > > > > > Cc: "freesurfer@nmr.mgh.harvard.edu" > > freesurfer@nmr.mgh.harvard.edu > > > > > > > Message-ID: > > alpine.LRH.2.03.1401052049480.16518@nmr.mgh.harvard.edu > > > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > > > > > > > Hi Katica > > > > > > > > > > > > > > what format was the input image to recon-all? Can you
verify
that > > > > tkmedit > > > > > > > has the directions correct (that is what it labels as
anterior
is > > > > actually > > > > > > > anatomically anterior, etc...). If so, then the
talairach
just
> > failed > > > > and > > > > > > > you will need to either try an alternative (like the
MNI
or
SPM > > > > > > talairachs) > > > > > > > or generate it manually. > > > > > > > > > > > > > > cheers > > > > > > > Bruce > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Thu, 2 Jan 2014, Boric, Katica A. > > > > > > > wrote: > > > > > > > > > > > > > > > Happy New Year freesuerfers! > > > > > > > > I run into this error while doing?recon-all : > > > > > > > > > > > > > > > > ERROR: talairach_afd: Talairach Transform: > > transforms/talairach.xfm > > > > > > > > ***FAILED*** (p=0.0000, pval=0.0000 <
threshold=0.0050)
> > > > > > > > Manual Talairach alignment may be necessary, or > > > > > > > > include the -notal-check flag to skip this test, > > > > > > > > making sure the -notal-check flag follows -all > > > > > > > > or -autorecon1 in the command string. > > > > > > > > > > > > > > > > I would really appreciate if someone could give me
some
advice > > on > > > > how to > > > > > > fix > > > > > > > > this error. > > > > > > > > > > > > > > > > Thank you very much! > > > > > > > > > > > > > > > > Katica Boric, > > > > > > > > > > > > > > > > > > > > > > > > ps:?Here is the error log: > > > > > > > > > > > > > > > > #@# Talairach Failure Detection Thu Jan ?2 14:20:32
EST
2014
> > > > > > > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > > > > > > > > > > > > > > > ?talairach_afd -T 0.005 -xfm
transforms/talairach.xfm?
> > > > > > > > > > > > > > > > ERROR: talairach_afd: Talairach Transform: > > transforms/talairach.xfm > > > > > > > > ***FAILED*** (p=0.0000, pval=0.0000 <
threshold=0.0050)
> > > > > > > > INFO: Attempting MINC mritotal to perform Talairach
align
> > > > > > > > #-------------------------------------------- > > > > > > > > #@# Talairach Thu Jan ?2 14:20:33 EST 2014 > > > > > > > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > > > > > > > > > > > > > > > ?mri_nu_correct.mni --n 1 --proto-iters 1000
--distance
50
> > > > --no-rescale > > > > > > --i > > > > > > > > orig.mgz --o orig_nu.mgz? > > > > > > > > > > > > > > > > > > > > > > > > ?talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm? > > > > > > > > > > > > > > > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > > > > > > > /usr/local/freesurfer/bin/talairach > > > > > > > > --i orig_nu.mgz --xfm transforms/talairach.auto.xfm > > > > > > > > $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ > > > > > > > > Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1
SMP
Tue
Jan > > 8 > > > > > > 20:57:42 > > > > > > > > UTC 2013 x86_64 x86_64 x86_64 GNU/Linux > > > > > > > > Thu Jan ?2 14:21:30 EST 2014 > > > > > > > > tmpdir is transforms/tmp.talairach.34005 > > > > > > > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > > > > > > > mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc > > > > > > > > mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc? > > > > > > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16
mreuter
Exp $ > > > > > > > > reading from orig_nu.mgz... > > > > > > > > TR=8.23, TE=3.22, TI=450.00, flip angle=12.00 > > > > > > > > i_ras = (-1, -9.03383e-08, 0) > > > > > > > > j_ras = (-1.3411e-07, 2.66591e-08, -1) > > > > > > > > k_ras = (1.59256e-07, 1, -5.93718e-09) > > > > > > > > writing to transforms/tmp.talairach.34005/src.mnc... > > > > > > > > -------------------------------------------- > > > > > > > > mritotal -verbose -debug -clobber -modeldir > > > > > > > > /usr/local/freesurfer/mni/bin/../share/mni_autoreg
-protocol
> > icbm > > > > > > > > transforms/tmp.talairach.34005/src.mnc > > transforms/talairach.auto.xfm > > > > > > > > Legacy library shellwords.pl will be removed from
the
Perl
core > > > > > > distribution > > > > > > > > in the next major release. Please install it from
the
CPAN
> > > > distribution > > > > > > > > Perl4::CoreLibs. It is being used at > > > > > > /usr/local/freesurfer/mni/bin/mritotal, > > > > > > > > line 460. > > > > > > > > ? > > > > > > > > ? > > > > > > > > Thu Jan ?2 14:21:43 EST 2014 > > > > > > > > talairach done > > > > > > > > > > > > > > > > ?cp transforms/talairach.auto.xfm
transforms/talairach.xfm?
> > > > > > > > > > > > > > > > #-------------------------------------------- > > > > > > > > #@# Talairach Failure Detection Thu Jan ?2 14:21:44
EST
2014
> > > > > > > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > > > > > > > > > > > > > > > ?talairach_afd -T 0.005 -xfm
transforms/talairach.xfm?
> > > > > > > > > > > > > > > > ERROR: talairach_afd: Talairach Transform: > > transforms/talairach.xfm > > > > > > > > ***FAILED*** (p=0.0000, pval=0.0000 <
threshold=0.0050)
> > > > > > > > Manual Talairach alignment may be necessary, or > > > > > > > > include the -notal-check flag to skip this test, > > > > > > > > making sure the -notal-check flag follows -all > > > > > > > > or -autorecon1 in the command string. > > > > > > > > See > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > > > > > > > > Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1
SMP
Tue
Jan > > 8 > > > > > > 20:57:42 > > > > > > > > UTC 2013 x86_64 x86_64 x86_64 GNU/Linux > > > > > > > > > > > > > > > > recon-all -s xxx_SurferOutput exited with ERRORS at
Thu
Jan
?2 > > > > 14:21:45 > > > > > > EST > > > > > > > > 2014 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------ > > > > > > > > > > > > > > Message: 7 > > > > > > > Date: Sun, 5 Jan 2014 23:35:55 -0800 > > > > > > > From: Frank Hsieh two.frank@gmail.com > > > > > > > Subject: [Freesurfer] ROI masks created in FreeSurfer
used
in
> > FSL?? > > > > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > > > > Message-ID: > > > > > > > > >
CABBeRCEt37ZwE1-jHuZGC3Vw-D_v2+svOAnQUcSP6kW37qT4oQ@mail.gmail.com
> > > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > > > > > > > Dear FreeSurfer Users, > > > > > > > > > > > > > > I ran recon -all on my structural image and created
ROI
masks
> > (using > > > > > > > mri_label2vol) based on FreeSurfer's cortical
parcellation.
I'd > > like > > > > to > > > > > > use > > > > > > > these masks for further analysis with FSL. However, it
seems
that > > the > > > > ROI > > > > > > > masks generated with mri_label2vol have different
header
> > information > > > > than > > > > > > > that of the original structural image. As a result, I
was
unable > > to > > > > carry > > > > > > > out further analysis with FSL (e.g., converting these
ROI
masks > > into > > > > > > > functional space with hires2example_func.mat). I was
wondering
if > > > > there is > > > > > > > a way to solve this issue. > > > > > > > > > > > > > > Many thanks in advance. > > > > > > > Frank > > > > > > > -------------- next part -------------- > > > > > > > An HTML attachment was scrubbed... > > >>>>>URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20
1
4
0 > > 1 > > > > 05/a > > > > > > 552481b/attachment-0001.html > > > > > > > > > > > > > > ------------------------------ > > > > > > > > > > > > > > Message: 8 > > > > > > > Date: Mon, 6 Jan 2014 17:11:54 +0900 > > > > > > > From: Muhammad Naveed Iqbal Qureshi
> > > > > > > Subject: [Freesurfer] converting .thickness files of
T1
MRI
from > > > > > > > FreeSurfer into AFNI > > > > > > > To: "freesurfer@nmr.mgh.harvard.edu" > > freesurfer@nmr.mgh.harvard.edu > > > > > > > Message-ID:
BLU174-W27296B6C59F4D34F89293AC4B70@phx.gbl
> > > > > > > Content-Type: text/plain; charset="ks_c_5601-1987" > > > > > > > > > > > > > > Hi, > > > > > > > I want to know that how can I convert FreeSurfer
.thickness
files > > to > > > > AFNI > > > > > > readable format > > > > > > > I tried the following Command but it gives error > > > > > > > > > > > > > > > > > > > > > mri_convert > > /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness > > > > > >
/media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik
> > > > > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16
mreuter
Exp
$ > > > > > > > reading from > > > > /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness... > > > > > > > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > > > > > > > i_ras = (-1, 0, 0) > > > > > > > j_ras = (0, 0, -1) > > > > > > > k_ras = (0, 1, 0) > > > > > > > writing to > > > > > > /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik... > > > > > > > AFNI BRIK write unsupported > > > > > > > ERROR: failure writing > > > > > >
/media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik
> > > > > > > UN:/media> > > > > > > > > > > > > > > Please let me help me to solve this problem > > > > > > > Thank you :) > > > > > > > > > > > > > > > > > > > > > > > > > > > > Best Regards, > > > > > > > > > > > > > > Muhammad > > > > > > > Naveed Iqbal Qureshi > > > > > > > > > > > > > > > > > > > > > -------------- next part -------------- > > > > > > > An HTML attachment was scrubbed... > > >>>>>URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20
1
4
0 > > 1 > > > > 06/1 > > > > > > d3fe803/attachment-0001.html > > > > > > > > > > > > > > ------------------------------ > > > > > > > > > > > > > > Message: 9 > > > > > > > Date: Mon, 6 Jan 2014 10:45:52 +0100 > > > > > > > From: "L. Schweren" l.j.s.schweren@umcg.nl > > > > > > > Subject: [Freesurfer] brain orientation in qdec > > > > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > > > > Message-ID: 005601cf0ac4$16bda9b0$4438fd10$@umcg.nl > > > > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > > > Dear experts, > > > > > > > > > > > > > > > > > > > > > > > > > > > > I ran recon-all with qcache. When loading the right
hemisphere
of > > > > > > fsaverage > > > > > > > (or any other surface reconstruction) into tksurfer
(for
example > > > > command: > > > > > > > tksurfer fsaverage rh white), the left hemisphere
surface
is
> > > > displayed, > > > > > > and > > > > > > > it is upside down. When I import annotations they load
in
the
same > > > > > > > orientation as the surface. However, the coordinates
and
the
> > labels, > > > > > > > displayed in the Tksurfer Tools window, are not. For
example,
when > > I > > > > move > > > > > > > the cursor to the temporal lobe, the label says it's postcentral. > > I do > > > > not > > > > > > > mind manually turning the surfaces in tksurfer, but I
do
need
to > > be > > > > sure I > > > > > > > am looking at the correct hemispheres, coordinates and
labels.
> > > > > > > > > > > > > > I hope you can help me solve this. Thank you in
advance.
> > > > > > > > > > > > > > > > > > > > > > > > > > > > Best wishes, > > > > > > > > > > > > > > Lizanne > > > > > > > > > > > > > > > > > > > > > > > > > > > > -------------- next part -------------- > > > > > > > An HTML attachment was scrubbed... > > >>>>>URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20
1
4
0 > > 1 > > > > 06/5 > > > > > > 583e136/attachment-0001.html > > > > > > > > > > > > > > ------------------------------ > > > > > > > > > > > > > > Message: 10 > > > > > > > Date: Mon, 6 Jan 2014 08:41:58 -0500 (EST) > > > > > > > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > > > > > > > Subject: Re: [Freesurfer] converting .thickness files
of
T1
MRI > > from > > > > > > > FreeSurfer into AFNI > > > > > > > To: Muhammad Naveed Iqbal Qureshi
> > > > > > > Cc: "freesurfer@nmr.mgh.harvard.edu" > > freesurfer@nmr.mgh.harvard.edu > > > > > > > Message-ID: > > alpine.LRH.2.03.1401060840550.16518@nmr.mgh.harvard.edu > > > > > > > Content-Type: text/plain; charset="iso-8859-15" > > > > > > > > > > > > > > Hi Muhammad > > > > > > > > > > > > > > try: > > > > > > > > > > > > > > set sdir=/home/naveed/freesurfer/subjects/CHR01/surf > > > > > > > mris_convert -c $sdir/rh.thickness $sdir/rh.orig > > > > $sdir/rh.thickness.brik > > > > > > > > > > > > > > cheers > > > > > > > Bruce > > > > > > > > > > > > > > On Mon, 6 Jan 2014, Muhammad Naveed Iqbal Qureshi
wrote:
> > > > > > > > > > > > > > > Hi, > > > > > > > > I want to know that how can I convert FreeSurfer
.thickness
> > files to > > > > > > AFNI > > > > > > > > readable format > > > > > > > > I tried the following Command but it gives error > > > > > > > > > > > > > > > > > > > > > > > > mri_convert > > /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness > > > > > > > > /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik > > > > > > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16
mreuter
Exp $ > > > > > > > > reading from > > > > /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness... > > > > > > > > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > > > > > > > > i_ras = (-1, 0, 0) > > > > > > > > j_ras = (0, 0, -1) > > > > > > > > k_ras = (0, 1, 0) > > > > > > > > writing to > > > > > > /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik... > > > > > > > > AFNI BRIK write unsupported > > > > > > > > ERROR: failure writing > > > > > > > > /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik > > > > > > > > UN:/media> > > > > > > > > > > > > > > > > Please let me help me to solve this problem > > > > > > > > Thank you :)? > > > > > > > > > > > > > > > > Best Regards, > > > > > > > > Muhammad Naveed Iqbal Qureshi > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------ > > > > > > > > > > > > > > Message: 11 > > > > > > > Date: Mon, 6 Jan 2014 10:40:43 -0500 (EST) > > > > > > > From: "Emad Ahmadi" emad@nmr.mgh.harvard.edu > > > > > > > Subject: [Freesurfer] recon-all error > > > > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > > > > Message-ID: > > 63234.172.19.2.113.1389022843.squirrel@mail.martinos.org > > > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > > > > > > > Hello & Happy New Year! > > > > > > > > > > > > > > I'm running recon-all for one subject on MGH clusters (ERISone), > > and > > > > it > > > > > > > exits with error. I would appreciate it if you help me
figure
out > > what > > > > the > > > > > > > problem is. The log file is attached. > > > > > > > > > > > > > > All the best throughout 2014! > > > > > > > Emad > > > > > > > > > > > > > > > > > > > > > Emad Ahmadi, MD > > > > > > > ------------------------------------------------ > > > > > > > Research Fellow > > > > > > > Department of Radiology > > > > > > > Massachusetts General Hospital > > > > > > > Harvard Medical School > > > > > > > > > > > > > > 25 New Chardon Street, Suite 400 > > > > > > > Boston, MA 02114 > > > > > > > Tel: 617 726 5237 > > > > > > > Email: emad@nmr.mgh.harvard.edu > > > > > > > > > > > > > > -------------- next part -------------- > > > > > > > A non-text attachment was scrubbed... > > > > > > > Name: recon-all.log > > > > > > > Type: application/octet-stream > > > > > > > Size: 20022 bytes > > > > > > > Desc: not available > > > >>>>Url:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/201
4
0
1 > > 06/ > > > > e > > > > > > 6358cca/attachment-0002.obj > > > > > > > -------------- next part -------------- > > > > > > > A non-text attachment was scrubbed... > > > > > > > Name: recon1job.bash > > > > > > > Type: application/octet-stream > > > > > > > Size: 1555 bytes > > > > > > > Desc: not available > > > >>>>Url:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/201
4
0
1 > > 06/ > > > > e > > > > > > 6358cca/attachment-0003.obj > > > > > > > > > > > > > > ------------------------------ > > > > > > > > > > > > > > Message: 12 > > > > > > > Date: Mon, 6 Jan 2014 17:51:18 +0200 > > > > > > > From: Rotem Saar saar.rotem@gmail.com > > > > > > > Subject: [Freesurfer] Fwd: Anatomical segmentation -
question
> > > > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > > > > Message-ID: > > > > > > > > >
CAMjFEmbcEwbXMOyxw-kuep6NSzdnk=rYHSEvwPGSbiXkBZKxtA@mail.gmail.com
> > > > > > > Content-Type: text/plain; charset="windows-1252" > > > > > > > > > > > > > > Dear freesurfer experts, > > > > > > > > > > > > > > I'm performing anatomical segmentation for Philips
dicoms
(3T
> > > > scanner). I > > > > > > > got these two images from the same slice while
performing
step
> > number > > > > 4 in > > > > > > > the script below ? from some reason, the two images
don't
fit.
> > Should > > > > I > > > > > > use > > > > > > > "scale brain" ? I know this is not recommended thus
want
to
> > consult > > > > with u > > > > > > > first ? Can u please comment on why this is happening?
Is
there > > any > > > > value > > > > > > > that corresponds to "how good is the segmentation" ?
if
yes,
where > > can > > > > I > > > > > > > find it ? > > > > > > > > > > > > > > My script is written below. > > > > > > > > > > > > > > Thanks, > > > > > > > > > > > > > > Rotem > > > > > > > > > > > > > > Anatomical segmentation: > > > > > > > > > > > > > > first step- 23 hours: > > > > > > > > > > > > > > *recon-all -autorecon-all -i ~/Desktop/ FOLDER-NAME /I00001.dcm -s > > > > > > > FOLDER-NAME* > > > > > > > > > > > > > > second step:(gyrus=green, sulcus=red) > > > > > > > > > > > > > > *tksurfer -curv FOLDER-NAME lh/rh inflated* > > > > > > > > > > > > > > third step: (talairch registretion) > > > > > > > > > > > > > > *tkmedit FOLDER-NAME brainmask.mgz* > > > > > > > > > > > > > > File-> transforms-> load transform AUX-> Browse->
talairch.xfm
> > > > > > > > > > > > > > forth step: (simetry - allows changing 12df
transformation. if
we > > made > > > > any > > > > > > > changes we should click "save reg" and run this
command
again)
> > > > > > > > > > > > > > *tkregister2 --mgz --s FOLDER-NAME --fstal --surf
orig*
> > > > > > > > > > > > > > IF WE CHANGE ANYTHING, CLICK "SAVE REG" AND RUN FROM
STARTING
> > POING: > > > > > > > recon-all -all -subjectid FOLDER-NAME > > > > > > > > > > > > > > fifth step: (scalp removal: if removed too much, rise
up
from
the > > > > value > > > > > > 25: > > > > > > > > > > > > > > *recon-all -skullstrip -wsthresh 25 -clean-bm
-no-wsgcaatlas
-s > > > > > > > FOLDER-NAME * > > > > > > > > > > > > > > to check the result press: *tkmedit FOLDER-NAME
brainmask.mgz
> > lh.white > > > > > > -aux > > > > > > > T1.mgz -aux-surface rh.white *) > > > > > > > > > > > > > > for hand correction: *tkmedit FOLDER-NAME
brainmask.mgz
-aux
> > T1.mgz* > > > > > > > > > > > > > > tools-> configure volume brush -> MARK: mode=clone,
source=Aux
> > > > > > > > > > > > > > tools-> configure brush info (for choosing brush size) > > > > > > > > > > > > > > click on edit voxels: click in MIDDLE for adding
voxels,
RIGHT
for > > > > > > removing > > > > > > > voxels : slice by slice. > > > > > > > > > > > > > > when finish, click: File-> save main volume > > > > > > > > > > > > > > sisxt step: (cp for correcting segmentation) > > > > > > > > > > > > > > *tkmedit FOLDER-NAME brainmask.mgz lh.white -aux
T1.mgz
> > -aux-surface > > > > > > > rh.white* > > > > > > > > > > > > > > seventh step: (done) > > > > > > > > > > > > > > *recon-all -autorecon2-cp -autorecon3 -s FOLDER-NAME* > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Rotem Saar-Ashkenazy > > > > > > > Department of Brain and Cognitive Science > > > > > > > Ben Gurion University of the Negev > > > > > > > Beer-Sheva 84105 > > > > > > > Israel > > > > > > > -------------- next part -------------- > > > > > > > An HTML attachment was scrubbed... > > >>>>>URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20
1
4
0 > > 1 > > > > 06/3 > > > > > > df4f7b3/attachment.html > > > > > > > -------------- next part -------------- > > > > > > > A non-text attachment was scrubbed... > > > > > > > Name: 3.png > > > > > > > Type: image/png > > > > > > > Size: 299694 bytes > > > > > > > Desc: not available > > > >>>>Url:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/201
4
0
1 > > 06/ > > > > 3 > > > > > > df4f7b3/attachment.png > > > > > > > > > > > > > > ------------------------------ > > > > > > > > > > > > > > _______________________________________________ > > > > > > > Freesurfer mailing list > > > > > > > Freesurfer@nmr.mgh.harvard.edu > > > > > > >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > > > > > > > > > > > End of Freesurfer Digest, Vol 119, Issue 6 > > > > > > > ****************************************** > > > > > > > > > > > > > > > > > > > > > > > >
hmmm, I'm not sure what is going on then. Make sure that your path in the mri_surf2vol command line is correct for the orig.mgz I guess. Other than that, maybe Doug can comment? On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
I am sorry i gave the wrong command: following is the result: UN:~/CHR01> mri_info mri/orig.mgz Volume information for mri/orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 1670.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = 0.0000, c_r = -0.3715 : x_a = 0.0000, y_a = -0.0000, z_a = 1.0000, c_a = 18.5846 : x_s = -0.0000, y_s = -1.0000, z_s = -0.0000, c_s = 6.4364 talairach xfm : mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 -0.0000 0.0000 127.6285 0.0000 -0.0000 1.0000 -109.4154 -0.0000 -1.0000 -0.0000 134.4364 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 0.0000 0.0000 127.6285 0.0000 0.0000 -1.0000 134.4364 0.0000 1.0000 0.0000 109.4154 0.0000 0.0000 0.0000 1.0000
Best Regards, Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:43:27 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
something is wrong with that file. Can you check permissions on it and size?
On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
This is the output : UN:~/CHR01/mri> mri_info mri/orig.mgz mghRead(mri/orig.mgz, -1): could not open file
What did I missed while processing?
Best Regards, Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:38:36 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
can you run
mri_info mri/orig.mgz On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
yes as you can see below: UN:~/CHR01/mri> ls aparc.a2009s+aseg.mgz orig aparc+aseg.mgz orig.mgz aseg.auto.mgz orig_nu.log aseg.auto_noCCseg.label_intensities.txt orig_nu.mgz aseg.auto_noCCseg.mgz rawavg.mgz aseg.mgz rh.ribbon.mgz brain.finalsurfs.mgz ribbon.mgz brainmask.auto.mgz segment.dat brainmask.mgz T1.mgz brain.mgz talairach.label_intensities.txt ctrl_pts.mgz talairach.log filled.mgz talairach_with_skull_2.log lh.ribbon.mgz talairach_with_skull.log mri_nu_correct.mni.log transforms mri_nu_correct.mni.log.bak wm.asegedit.mgz norm.mgz wm.mgz nu.mgz wmparc.mgz nu_noneck.mgz wm.seg.mgz UN:~/CHR01/mri>
Best Regards, Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:34:20 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
does mri/orig.mgz exist? On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
> Now another error > > UN:~> mri_surf2vol --surfval surf/rh.thickness paint --hemi rh
--fillribbon
> --template mri/orig.mgz --volregidentity {$subj} --outvol > {$subj}_rh.ribbon.nii > gdiagno = -1 > Using identity matrix for registration > mghRead(mri/orig.mgz, -1): could not open file > mri_surf2vol ERROR: reading mri/orig.mgz header > > > Best Regards, > Muhammad Naveed Iqbal Qureshi > Ph.D. Candidate > Bio-Medical Signal & System Analysis Laboratory > Department of Medical System Engineering > Gwangju Institute of Sciences and Technology > 123, Cheomdangwagi-ro, Buk-gu, Gwangju, 500-712, Republic of
Korea
> Tel : +82-62-715-3266 > Email : mniqureshi@gist.ac.kr > URL : http://bmssa.gist.ac.kr > P please don't print this e-mail unless you really need to > > > > > Date: Tue, 7 Jan 2014 08:26:56 -0500 > > From: fischl@nmr.mgh.harvard.edu > > To: mniqureshi@hotmail.com > > CC: freesurfer@nmr.mgh.harvard.edu > > Subject: RE: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6 > > > > sorry, I wasn't clear. Try: > > > > mri_surf2vol --surfval surf/rh.thickness paint --hemi rh
--fillribbon
\
> > --template mri/orig.mgz --volregidentity {$subj} --outvol > {$subj}_rh.ribbon.nii > > > > On > > Tue, 7 Jan 2014, Muhammad Naveed Iqbal > > Qureshi wrote: > > > > > Still the same error > > > > > > UN:~> mri_surf2vol --surfval surf/rh.thickness.paint --hemi
rh
> --fillribbon > > > --template mri/orig.mgz --volregidentity {$subj} --outvol > > > {$subj}_rh.ribbon.nii > > > gdiagno = -1 > > > ERROR: cannot recognize the type of surf/rh.thickness.paint > > > > > > > > > Best Regards, > > > Muhammad Naveed Iqbal Qureshi > > > > > > > > > > Date: Tue, 7 Jan 2014 08:20:43 -0500 > > > > From: fischl@nmr.mgh.harvard.edu > > > > To: mniqureshi@hotmail.com > > > > CC: freesurfer@nmr.mgh.harvard.edu > > > > Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119,
Issue 6
> > > > > > > > try adding "paint" after "surf/rh.thickness". The -surfval
switch
> takes an > > > > optional format parameter after the file name I think > > > > > > > > cheers > > > > Bruce > > > > > > > > On Tue, 7 Jan 2014, Muhammad > > > > Naveed Iqbal Qureshi wrote: > > > > > > > > > Hi Bruce, > > > > > I have tried to convert by using the following commands
but
still
> some > > > error > > > > > occur. > > > > > > > > > > UN:~> set subj=/home/naveed/freesurfer/subjects/CHR01/ > > > > > UN:~> mri_surf2vol --surfval surf/rh.thickness --hemi rh > --fillribbon > > > > > --template mri/orig.mgz --volregidentity {$subj}
--outvol
> > > > > {$subj}_rh.ribbon.nii > > > > > gdiagno = -1 > > > > > ERROR: cannot recognize the type of surf/rh.thickness > > > > > > > > > > Can you help me. > > > > > Thank you. > > > > > > > > > > Best Regards, > > > > > Muhammad Naveed Iqbal Qureshi > > > > > > > > > > > > > > > > Date: Tue, 7 Jan 2014 08:13:45 -0500 > > > > > > From: fischl@nmr.mgh.harvard.edu > > > > > > To: mniqureshi@hotmail.com > > > > > > CC: freesurfer@nmr.mgh.harvard.edu > > > > > > Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119,
Issue 6
> > > > > > > > > > > > Hi Muhammad > > > > > > > > > > > > have you looked at the help? It's pretty extensive. If
you
have
> > > trouble > > > > > > post again and Doug should be able to guide you > > > > > > > > > > > > cheers > > > > > > Bruce > > > > > > On Tue, 7 Jan 2014, Muhammad > > > > > > Naveed Iqbal Qureshi wrote: > > > > > > > > > > > > > Thank you Bruce, > > > > > > > > > > > > > > Please guide me how can I use mri_surf2vol
command on
> > > lh/rh.thickness > > > > > files > > > > > > > to get the output as lh/rh.ribbon.nii for AFNI SUMA. > > > > > > > Thank you > > > > > > > > > > > > > > Best Regards, > > > > > > > Muhammad Naveed Iqbal Qureshi > > > > > > > > > > > > > > > From: freesurfer-request@nmr.mgh.harvard.edu > > > > > > > > Subject: Freesurfer Digest, Vol 119, Issue 6 > > > > > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > > > > > Date: Mon, 6 Jan 2014 10:51:33 -0500 > > > > > > > > > > > > > > > > Send Freesurfer mailing list submissions to > > > > > > > > freesurfer@nmr.mgh.harvard.edu > > > > > > > > > > > > > > > > To subscribe or unsubscribe via the World Wide
Web,
visit
> > > > > > > >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > > > > > or, via email, send a message with subject or body
'help'
to
> > > > > > > > freesurfer-request@nmr.mgh.harvard.edu > > > > > > > > > > > > > > > > You can reach the person managing the list at > > > > > > > > freesurfer-owner@nmr.mgh.harvard.edu > > > > > > > > > > > > > > > > When replying, please edit your Subject line so it
is
more
> > > specific > > > > > > > > than "Re: Contents of Freesurfer digest..." > > > > > > > > > > > > > > > > > > > > > > > > Today's Topics: > > > > > > > > > > > > > > > > 1. erroneuos segmentation labeling of skull
outside of
brain
> > > > > > > > (Yuliya Yoncheva) > > > > > > > > 2. Re: erroneuos segmentation labeling of skull
outside of
> brain > > > > > > > > (Bruce Fischl) > > > > > > > > 3. Re: Motion correction for SPACE FLAIR (Bruce
Fischl)
> > > > > > > > 4. Re: erroneuos segmentation labeling of skull
outside of
> brain > > > > > > > > (Yuliya Yoncheva) > > > > > > > > 5. Re: erroneuos segmentation labeling of skull
outside of
> brain > > > > > > > > (Bruce Fischl) > > > > > > > > 6. Re: recon-all exited w/errors (Bruce Fischl) > > > > > > > > 7. ROI masks created in FreeSurfer used in FSL??
(Frank
Hsieh)
> > > > > > > > 8. converting .thickness files of T1 MRI from
FreeSurfer
into
> > > > > > > > AFNI (Muhammad Naveed Iqbal Qureshi) > > > > > > > > 9. brain orientation in qdec (L. Schweren) > > > > > > > > 10. Re: converting .thickness files of T1 MRI from
FreeSurfer
> > > > > > > > into AFNI (Bruce Fischl) > > > > > > > > 11. recon-all error (Emad Ahmadi) > > > > > > > > 12. Fwd: Anatomical segmentation - question (Rotem
Saar)
> > > > > > > > > > > > > > > > > > > > > > > > > > >
> > > > > > > > > > > > > > > > Message: 1 > > > > > > > > Date: Sun, 5 Jan 2014 15:14:39 -0500 > > > > > > > > From: Yuliya Yoncheva yuliya.yoncheva@gmail.com > > > > > > > > Subject: [Freesurfer] erroneuos segmentation
labeling
of
skull
> > > outside > > > > > > > > of brain > > > > > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > > > > > Message-ID: > > > > > > > > > > >
CAGE5uFc2uD9pMefXjRZE0LQP+GcfhHKWeVkHxOGwDzV1=jYrQA@mail.gmail.com
> > > > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > > > > > > > > > Dear FreeSurfer community, > > > > > > > > > > > > > > > > I am visually inspecting the quality of my recon
-all
output
> for a > > > > > large > > > > > > > > dataset and have a rookie question. > > > > > > > > > > > > > > > > In some instances, when skull stripping ended up
leaving
some
> of > > > the > > > > > > > skull, > > > > > > > > these voxels are associated with a "sgmtn label"
(cerebral
> > > cortex). In > > > > > > > > other instances, although there are a small number
of
skull
> voxels > > > > > that > > > > > > > > were not removed automatically, these voxels do
not
have
an
> > > associated > > > > > > > > "sgmnt label" available in TkMedit Tools. > > > > > > > > > > > > > > > > Is it the case that only the voxels for which
there is
a
> > > segmentation > > > > > > > label > > > > > > > > are actually added to the total grey volume
estimate?
> > > > > > > > > > > > > > > > Thus, voxels, which have not been automatically
labelled
would
> not > > > > > impact > > > > > > > > volume computations? > > > > > > > > > > > > > > > > Thank you kindly for your help. > > > > > > > >
I think there might still be something wrong with the mri/orig.mgz, try this command to see if it is ok
mri_convert mri/orig.mgz deleteme.mgz
doug
On 01/07/2014 09:01 AM, Bruce Fischl wrote:
hmmm, I'm not sure what is going on then. Make sure that your path in the mri_surf2vol command line is correct for the orig.mgz I guess. Other than that, maybe Doug can comment? On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
I am sorry i gave the wrong command: following is the result:
UN:~/CHR01> mri_info mri/orig.mgz Volume information for mri/orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 1670.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = 0.0000, c_r = -0.3715 : x_a = 0.0000, y_a = -0.0000, z_a = 1.0000, c_a = 18.5846 : x_s = -0.0000, y_s = -1.0000, z_s = -0.0000, c_s = 6.4364 talairach xfm : mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 -0.0000 0.0000 127.6285 0.0000 -0.0000 1.0000 -109.4154 -0.0000 -1.0000 -0.0000 134.4364 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 0.0000 0.0000 127.6285 0.0000 0.0000 -1.0000 134.4364 0.0000 1.0000 0.0000 109.4154 0.0000 0.0000 0.0000 1.0000
Best Regards, Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:43:27 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
something is wrong with that file. Can you check permissions on it and size?
On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
This is the output :
UN:~/CHR01/mri> mri_info mri/orig.mgz mghRead(mri/orig.mgz, -1): could not open file
What did I missed while processing?
Best Regards, Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:38:36 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
can you run
mri_info mri/orig.mgz On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
yes as you can see below:
UN:~/CHR01/mri> ls aparc.a2009s+aseg.mgz orig aparc+aseg.mgz orig.mgz aseg.auto.mgz orig_nu.log aseg.auto_noCCseg.label_intensities.txt orig_nu.mgz aseg.auto_noCCseg.mgz rawavg.mgz aseg.mgz rh.ribbon.mgz brain.finalsurfs.mgz ribbon.mgz brainmask.auto.mgz segment.dat brainmask.mgz T1.mgz brain.mgz talairach.label_intensities.txt ctrl_pts.mgz talairach.log filled.mgz talairach_with_skull_2.log lh.ribbon.mgz talairach_with_skull.log mri_nu_correct.mni.log transforms mri_nu_correct.mni.log.bak wm.asegedit.mgz norm.mgz wm.mgz nu.mgz wmparc.mgz nu_noneck.mgz wm.seg.mgz UN:~/CHR01/mri>
Best Regards, Muhammad Naveed Iqbal Qureshi
> Date: Tue, 7 Jan 2014 08:34:20 -0500 > From: fischl@nmr.mgh.harvard.edu > To: mniqureshi@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6 > > does mri/orig.mgz exist? > On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi > wrote: > > > Now another error > > > > UN:~> mri_surf2vol --surfval surf/rh.thickness paint
--hemi rh
--fillribbon > > --template mri/orig.mgz --volregidentity {$subj} --outvol > > {$subj}_rh.ribbon.nii > > gdiagno = -1 > > Using identity matrix for registration > > mghRead(mri/orig.mgz, -1): could not open file > > mri_surf2vol ERROR: reading mri/orig.mgz header > > > > > > Best Regards, > > Muhammad Naveed Iqbal Qureshi > > Ph.D. Candidate > > Bio-Medical Signal & System Analysis Laboratory > > Department of Medical System Engineering > > Gwangju Institute of Sciences and Technology > > 123, Cheomdangwagi-ro, Buk-gu, Gwangju, 500-712, Republic of
Korea
> > Tel : +82-62-715-3266 > > Email : mniqureshi@gist.ac.kr > > URL : http://bmssa.gist.ac.kr > > P please don't print this e-mail unless you really need to > > > > > > > > > Date: Tue, 7 Jan 2014 08:26:56 -0500 > > > From: fischl@nmr.mgh.harvard.edu > > > To: mniqureshi@hotmail.com > > > CC: freesurfer@nmr.mgh.harvard.edu > > > Subject: RE: [Freesurfer] Freesurfer Digest, Vol 119,
Issue 6
> > > > > > sorry, I wasn't clear. Try: > > > > > > mri_surf2vol --surfval surf/rh.thickness paint --hemi rh
--fillribbon
\ > > > --template mri/orig.mgz --volregidentity {$subj} --outvol > > {$subj}_rh.ribbon.nii > > > > > > On > > > Tue, 7 Jan 2014, Muhammad Naveed Iqbal > > > Qureshi wrote: > > > > > > > Still the same error > > > > > > > > UN:~> mri_surf2vol --surfval surf/rh.thickness.paint
--hemi rh
> > --fillribbon > > > > --template mri/orig.mgz --volregidentity {$subj}
--outvol
> > > > {$subj}_rh.ribbon.nii > > > > gdiagno = -1 > > > > ERROR: cannot recognize the type of
surf/rh.thickness.paint
> > > > > > > > > > > > Best Regards, > > > > Muhammad Naveed Iqbal Qureshi > > > > > > > > > > > > > Date: Tue, 7 Jan 2014 08:20:43 -0500 > > > > > From: fischl@nmr.mgh.harvard.edu > > > > > To: mniqureshi@hotmail.com > > > > > CC: freesurfer@nmr.mgh.harvard.edu > > > > > Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119,
Issue 6
> > > > > > > > > > try adding "paint" after "surf/rh.thickness". The
-surfval
switch
> > takes an > > > > > optional format parameter after the file name I think > > > > > > > > > > cheers > > > > > Bruce > > > > > > > > > > On Tue, 7 Jan 2014, Muhammad > > > > > Naveed Iqbal Qureshi wrote: > > > > > > > > > > > Hi Bruce, > > > > > > I have tried to convert by using the following
commands but
still > > some > > > > error > > > > > > occur. > > > > > > > > > > > > UN:~> set
subj=/home/naveed/freesurfer/subjects/CHR01/
> > > > > > UN:~> mri_surf2vol --surfval surf/rh.thickness
--hemi rh
> > --fillribbon > > > > > > --template mri/orig.mgz --volregidentity {$subj}
--outvol
> > > > > > {$subj}_rh.ribbon.nii > > > > > > gdiagno = -1 > > > > > > ERROR: cannot recognize the type of
surf/rh.thickness
> > > > > > > > > > > > Can you help me. > > > > > > Thank you. > > > > > > > > > > > > Best Regards, > > > > > > Muhammad Naveed Iqbal Qureshi > > > > > > > > > > > > > > > > > > > Date: Tue, 7 Jan 2014 08:13:45 -0500 > > > > > > > From: fischl@nmr.mgh.harvard.edu > > > > > > > To: mniqureshi@hotmail.com > > > > > > > CC: freesurfer@nmr.mgh.harvard.edu > > > > > > > Subject: Re: [Freesurfer] Freesurfer Digest,
Vol 119,
Issue 6
> > > > > > > > > > > > > > Hi Muhammad > > > > > > > > > > > > > > have you looked at the help? It's pretty
extensive. If you
have > > > > trouble > > > > > > > post again and Doug should be able to guide you > > > > > > > > > > > > > > cheers > > > > > > > Bruce > > > > > > > On Tue, 7 Jan 2014, Muhammad > > > > > > > Naveed Iqbal Qureshi wrote: > > > > > > > > > > > > > > > Thank you Bruce, > > > > > > > > > > > > > > > > Please guide me how can I use mri_surf2vol
command on
> > > > lh/rh.thickness > > > > > > files > > > > > > > > to get the output as lh/rh.ribbon.nii for
AFNI SUMA.
> > > > > > > > Thank you > > > > > > > > > > > > > > > > Best Regards, > > > > > > > > Muhammad Naveed Iqbal Qureshi > > > > > > > > > > > > > > > > > From: freesurfer-request@nmr.mgh.harvard.edu > > > > > > > > > Subject: Freesurfer Digest, Vol 119, Issue 6 > > > > > > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > > > > > > Date: Mon, 6 Jan 2014 10:51:33 -0500 > > > > > > > > > > > > > > > > > > Send Freesurfer mailing list submissions to > > > > > > > > > freesurfer@nmr.mgh.harvard.edu > > > > > > > > > > > > > > > > > > To subscribe or unsubscribe via the World Wide
Web,
visit
> > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > or, via email, send a message with subject
or body
'help'
to > > > > > > > > > freesurfer-request@nmr.mgh.harvard.edu > > > > > > > > > > > > > > > > > > You can reach the person managing the list at > > > > > > > > > freesurfer-owner@nmr.mgh.harvard.edu > > > > > > > > > > > > > > > > > > When replying, please edit your Subject
line so it is
more
> > > > specific > > > > > > > > > than "Re: Contents of Freesurfer digest..." > > > > > > > > > > > > > > > > > > > > > > > > > > > Today's Topics: > > > > > > > > > > > > > > > > > > 1. erroneuos segmentation labeling of skull
outside of
brain > > > > > > > > > (Yuliya Yoncheva) > > > > > > > > > 2. Re: erroneuos segmentation labeling of
skull
outside of
> > brain > > > > > > > > > (Bruce Fischl) > > > > > > > > > 3. Re: Motion correction for SPACE FLAIR
(Bruce
Fischl)
> > > > > > > > > 4. Re: erroneuos segmentation labeling of
skull
outside of
> > brain > > > > > > > > > (Yuliya Yoncheva) > > > > > > > > > 5. Re: erroneuos segmentation labeling of
skull
outside of
> > brain > > > > > > > > > (Bruce Fischl) > > > > > > > > > 6. Re: recon-all exited w/errors (Bruce
Fischl)
> > > > > > > > > 7. ROI masks created in FreeSurfer used in
FSL??
(Frank
Hsieh) > > > > > > > > > 8. converting .thickness files of T1 MRI from
FreeSurfer
into > > > > > > > > > AFNI (Muhammad Naveed Iqbal Qureshi) > > > > > > > > > 9. brain orientation in qdec (L. Schweren) > > > > > > > > > 10. Re: converting .thickness files of T1
MRI from
FreeSurfer > > > > > > > > > into AFNI (Bruce Fischl) > > > > > > > > > 11. recon-all error (Emad Ahmadi) > > > > > > > > > 12. Fwd: Anatomical segmentation - question
(Rotem
Saar)
> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >
> > > > > > > > > > > > > > > > > > Message: 1 > > > > > > > > > Date: Sun, 5 Jan 2014 15:14:39 -0500 > > > > > > > > > From: Yuliya Yoncheva
> > > > > > > > > Subject: [Freesurfer] erroneuos segmentation
labeling
of
skull > > > > outside > > > > > > > > > of brain > > > > > > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > > > > > > Message-ID: > > > > > > > > > > > > >
CAGE5uFc2uD9pMefXjRZE0LQP+GcfhHKWeVkHxOGwDzV1=jYrQA@mail.gmail.com
> > > > > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > > > > > > > > > > > Dear FreeSurfer community, > > > > > > > > > > > > > > > > > > I am visually inspecting the quality of my
recon -all
output > > for a > > > > > > large > > > > > > > > > dataset and have a rookie question. > > > > > > > > > > > > > > > > > > In some instances, when skull stripping
ended up
leaving
some > > of > > > > the > > > > > > > > skull, > > > > > > > > > these voxels are associated with a "sgmtn
label"
(cerebral
> > > > cortex). In > > > > > > > > > other instances, although there are a small
number of
skull > > voxels > > > > > > that > > > > > > > > > were not removed automatically, these
voxels do not
have
an > > > > associated > > > > > > > > > "sgmnt label" available in TkMedit Tools. > > > > > > > > > > > > > > > > > > Is it the case that only the voxels for which
there is
a
> > > > segmentation > > > > > > > > label > > > > > > > > > are actually added to the total grey volume
estimate?
> > > > > > > > > > > > > > > > > > Thus, voxels, which have not been
automatically
labelled
would > > not > > > > > > impact > > > > > > > > > volume computations? > > > > > > > > > > > > > > > > > > Thank you kindly for your help. > > > > > > > > >
freesurfer@nmr.mgh.harvard.edu