Freesurfer

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Re: [Freesurfer] Optic chiasm resisting edits
by Peter McNally 31 Jul '12

31 Jul '12

Whoops forgot to select reply all... Yes I am erasing the chiasm using tkmedit--I'll rerun autorecon-wm now and send the recon-all.log results when they finish (probably) tomorrow. Thank you, Peter On Tue, Jul 31, 2012 at 2:34 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > can you cc the list on these emails? And try rerunning autorecon2-wm and > send us the recon-all.log results? You are erasing the chiasm using > tkmedit, aren't you? > > > On Tue, 31 Jul 2012, Peter McNally wrote: > > The edits do not appear to be reflected in the filled.mgz (the chiasm is >> still present on the filled.mgz volume). The same is true for ?h.orig, and >> they are even worse than normal on ?h.orig.nofix. >> >> On Tue, Jul 31, 2012 at 2:14 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu >> > >> wrote: >> hmmm. And are the edits reflected in the filled.mgz? Is the >> chiasm gone? How about in the ?h.orig and ?h.orig.nofix? >> On Tue, 31 Jul 2012, Peter McNally wrote: >> >> Hi Bruce, >> >> Thank you for your speedy response. Yes, I ran >> -autorecon2-wm -autorecon3. >> >> Best, >> Peter >> >> On Tue, Jul 31, 2012 at 2:03 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> Hi Peter >> what did you run after editing it out of the >> wm.mgz? You should >> be running -autorecon2-wm -autorecon3 >> >> cheers >> Bruce >> >> >> On Tue, 31 Jul 2012, Peter McNally wrote: >> >> Dear FreeSurfer Experts, >> >> I am using Freesurfer version 5.1 over >> at the >> University of Pennsylvania, >> and I have been running into issues with >> the optic >> chiasm. Despite having >> edited it out on both the brainmask.mgz >> and wm.mgz >> volumes, FreeSurfer has >> been insisting that it be included as a >> surface on >> multiple participants. >> Does anyone know a way to resolve this? >> Thank you >> very much for your time. >> >> Best, >> Peter McNally >> >> >> PS: I have included an example as an >> attachment >> (.pdf) >> >> >> >> >> >> >> 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<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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Re: [Freesurfer] Recon-all -qcache curvature error & recon-all make -all
by Gibbard, Clare 31 Jul '12

31 Jul '12

Hi Bruce, Thanks, I've attached the end of the recon-all.log file for one of the subjects (the whole thing was too large). This is what I get when I run recon-all -version: $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ When I try to run recon-all -s subject_no -make all I don't think anything comes up in the log. I get this in the terminal window: clare@clare-OptiPlex-990:~/subjects$ recon-all -s subject_20 -make all Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Subject 'subject_20': make all make: Nothing to be done for `all'. clare@clare-OptiPlex-990:~/subjects$ Let me know if you need anything else. Thank you. Best wishes, Clare ________________________________________ From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] Sent: 25 July 2012 14:44 To: Gibbard, Clare Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all -qcache curvature error & recon-all make -all Hi Clare can you send us the screen output and also what version you are running? thanks Bruce On Wed, 25 Jul 2012, Gibbard, Clare wrote: > Hello, > > I have run several scans using recon-all -all -subjid subject_no -expert > expert.opts where my expert.opts file changes the parameters for the > mri_normalize step (this works well in my scans). I then had to edit a few > of the scans by adding in more white matter and a few control points. I > re-ran them to incorporate the edits using recon-all -s subject_no -make all > -xopts-use. This worked well. > > I then ran recon-all -s subject_no -qcache ready for doing a group > analysis. I got an error reading the curvature file in those subjects I had > edited. I can see from the mailing list that others have had this error > previously and ran recon-all -s subject_no -make all to fix it. I tried > this, but I got a message saying that there was nothing to be done for all. > > Are you able to advise me on what I can try now? Do I need to go back a > step? > > Thank you very much, > Clare > > 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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Re: [Freesurfer] Label to ROI volume
by mmoayedi＠uhnres.utoronto.ca 31 Jul '12

31 Jul '12

Dear Dr. Fischl, Thank you for your respone. What would the --reg and the --temp be in this case? Massieh > ---------------- Original message ------------------ >From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >To: mmoayedi(a)uhnres.utoronto.ca-> >cc: freesurfer(a)nmr.mgh.harvard.edu-> >Subject: Re: [Freesurfer] Label to ROI volume > > try mri_label2vol (assuming by 'ROI' you mean a 3D volume) > > On Mon, 30 Jul 2012, mmoayedi(a)uhnres.utoronto.ca wrote: > > > > > Dear FS Experts, > > > > I have run recon-all on my subjects. I'm looking to convert the V1 and > various BA labels to ROIs in 3D anatomical space (orig.mgz). How would I > convert my freesufer label files to ROIs. Thank you! > > > > Massieh Moayedi > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > 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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Optic chiasm resisting edits
by Peter McNally 31 Jul '12

31 Jul '12

Dear FreeSurfer Experts, I am using Freesurfer version 5.1 over at the University of Pennsylvania, and I have been running into issues with the optic chiasm. Despite having edited it out on both the brainmask.mgz and wm.mgz volumes, FreeSurfer has been insisting that it be included as a surface on multiple participants. Does anyone know a way to resolve this? Thank you very much for your time. Best, Peter McNally PS: I have included an example as an attachment (.pdf)

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Issues with Tracula
by Sergio Medina 31 Jul '12

31 Jul '12

Hi! First of all let me thank you for having put at our disposal such great tools as FreeSurfer and Tracula! I am trying to run Tracula on the sample data that is on the website, but I've been running into some issues. I am attaching the configuration file just in case (dmrirc_single_subject-serch). The first step "trac-all -prep" seems to run fine. The first problem comes with the second step "trac-all -bedp". The complete trace is included in the attached file 1-error-trac-all-bedp.txt After finding this on the FreeSurfer mailing list https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/024042.htmlI changed the lines *${BPDIR}/fsl_sub_seychelles* for *${FSL_BIN}/fsl_sub* in the bedpostx_seychelles and I could continue, until the script seems to be stuck *Queuing parallel processing stage /volatile/tracula/results/**Diff001/dmri.bedpostX/monitor 0 slices processed 1 slices processed 1 slices processed 1 slices processed <== this line keeps on repeating* Following a suggestion I found on this other archived email http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20815.html I ran bedpostx on the dmri directory and seemed to succeed. I am attaching the output (2-bedpostx-dmri.txt). Then I tried to run trac-all -path but it stops with the following error: *niiRead(): error opening file /volatile/tracula/results/** Diff001/dmri.bedpostX/merged_**ph1samples.nii.gz ERROR: Could not read /volatile/tracula/results/** Diff001/dmri.bedpostX/merged_**ph1samples.nii.gz* I searched for that file everywhere but it doesn't exist. The closest I found was results/Diff001/dmri.bedpostX/merged_ph2samples.nii.gz Just in case I tried once again to run trac-all -bedp and this time, after having run bedpostx on the dmri directory, I get the following error (the whole output is in the attached 4-error-trac-all-bedp-2.txt file): *[...] slice 62 has already been processed slice 63 has already been processed wc: /volatile/tracula/results/**Diff001/dmri.bedpostX/**commands.txt: No such file or directory Queuing post processing stage 64 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. kill: 390: No such process* I tried searching for a file named commands.txt but I couldn't find any. Here is the output of bugr: *FREESURFER_HOME: /i2bm/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Debian version: squeeze/sid Kernel info: Linux 2.6.38-14-generic x86_64* and the output of source $FREESURFER_HOME/SetUpFreeSurfer.sh *-------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /i2bm/local/freesurfer FSFAST_HOME /i2bm/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /volatile/tracula/data/buckner_data/tutorial_subjs/ MNI_DIR /i2bm/local/freesurfer/mni FSL_DIR /usr/share/fsl/4.1* Thanks in advance for your help, any hint would be highly appreciated. Best, Sergio. -- Sergio Medina Engineer INRIA Parietal - Neurospin Bât 145, Point Courrier 156 91191 Gif/Yvette, France Tel.: (+33) 1 69 08 80 85

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tracula error...
by Gonzalo Rojas Costa 31 Jul '12

31 Jul '12

Hi: I ran "trac-all -prep -c dmrirc" and it finished ok... Then, when I tried to run the command "trac-all -bedp -c dmrirc", I got the error: ln -sf /usr/local/freesurfer/subjects/bmvf_23_7_2012/dlabel/diff/anat_brain_mask.bbr.nii.gz /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri/nodif_brain_mask.nii.gz ln -sf /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri/dwi.nii.gz /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri/data.nii.gz WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_seychelles /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri subjectdir is /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri Making bedpostx directory structure Queuing preprocessing stages [: 223: NONE: unexpected operator [: 314: NONE: unexpected operator [: 327: xbedpostx_pre: unexpected operator [: 486: x: unexpected operator [: 486: -le: argument expected Queuing parallel processing stage [: 223: NONE: unexpected operator [: 327: xbedpostx: unexpected operator [: 486: x27: unexpected operator 0 slices processed Queuing post processing stage [: 223: NONE: unexpected operator [: 314: NONE: unexpected operator [: 327: xbedpostx_post: unexpected operator [: 486: x: unexpected operator [: 486: -le: argument expected That problem occurr because my PC is not a parallelized environment?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Freesurfer GLM vs SPSS for voulme analysis
by Knut J Bjuland 31 Jul '12

31 Jul '12

Hi, I have calculated the group differences for volume using both FreeSurfer GLM and SPSS GLM. I have used gender and group as fixed factor and intercranial volume and age at MRI scan as covariate. GroupDescriptorFile 1 Title group_difference_between_group1_and_group2_gender_age DeMeanFlag 1 Class Group2Male Class Group2Female Class Group1Male Class Group1Female Variables ICU Age I used this as fsgd heading, and I used this contrast vector 0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 to be able to control for gender difference and difference due to age and ICU. I get difference results between SPSS and Freesurfer. I think this is strange since I used the same data both in FreeSurfer GLM and SPSS glm. Is there anything I have done wrong? I have used both univariate and multivariate in SPSS glm. Best regards Knut J

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Re: [Freesurfer] SUBJECTS_DIR not defined in environment
by Matthew Goldfinger 30 Jul '12

30 Jul '12

Ok the main email is CC'd. Below is what I did and the output I received. The goal is to get a brain volume, Subdural space and/or a CSF volume to estimate how much room for displacement/deformation the brain has. Thanks in advance for your help. Matthews-MacBook-Pro-2:~] matthew% printenv SUBJECTS_DIR /Applications/freesurfer/subjects [Matthews-MacBook-Pro-2:~] matthew% sudo mri_segstats --seg /Applications/freesurfer/subjects/bert/mri/aseg.mgz --sum /Applications/freesurfer/subjects/bert/stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --subject bert --brainmask mri/brainmask.mgz --brain-vol-from-seg $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg /Applications/freesurfer/subjects/bert/mri/aseg.mgz --sum /Applications/freesurfer/subjects/bert/stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /Applications/freesurfer/FreeSurferColorLUT.txt --subject bert --brainmask mri/brainmask.mgz --brain-vol-from-seg sysname Darwin hostname Matthews-MacBook-Pro-2.local machine x86_64 user root ERROR: SUBJECTS_DIR not defined in environment On Mon, Jul 30, 2012 at 10:38 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Matthew > Could you cc the list so others can answer? Can you also send us the > screen output showing exactly what you did? > Thanks > Bruce > > > > On Jul 30, 2012, at 8:19 PM, Matthew Goldfinger <mattgoldfinger(a)gmail.com> > wrote: > > Bruce, > When I execute printenv it gives me the correct path name > (/Applications/freesurfer/subjects). Upon original set up I automatically > sourced to freesurfersetup.csh as was described in the setup instructions. > How should I source to have Freesurfer commands available without running > into this problem? > > Matthew S. Goldfinger > > > > On Mon, Jul 30, 2012 at 8:02 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > >> Hi Matthew >> >> >> what shell are you using? If you type >> >> printenv SUBJECTS_DIR >> >> right before calling mri_segstats, what does it return? And when do you >> get that output? Are you sourcing the FreeSurferEnv.csh file? Don't execute >> it as otherwise it pushes a new shell, sets all that stuff, then pops out >> of it erasing all the stuff it set >> >> cheers >> Bruce >> >> >> >> On Mon, 30 Jul 2012, Matthew Goldfinger wrote: >> >> Dear Freesurfers, >>> Forgive me for asking about what appears to be a very simple issue >>> but I am stumped. I have defined my SUBJECTS_DIR as evidenced by this >>> output. >>> ----- freesurfer-Darwin-leopard-**i686-stable-pub-v5.1.0 -------- >>> Setting up environment for FreeSurfer/FS-FAST (and FSL) >>> FREESURFER_HOME /Applications/freesurfer >>> FSFAST_HOME /Applications/freesurfer/**fsfast >>> FSF_OUTPUT_FORMAT nii.gz >>> SUBJECTS_DIR /Applications/freesurfer/**subjects >>> MNI_DIR /Applications/freesurfer/mni >>> >>> But upon trying to execute the following: >>> mri_segstats --seg /Applications/freesurfer/**subjects/bert/mri/aseg.mgz >>> --sum >>> /Applications/freesurfer/**subjects/bert/stats/aseg.stats --pv >>> mri/norm.mgz >>> --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in >>> mri/norm.mgz --in-intensity-name norm --etiv --surf-wm-vol --surf-ctx-vol >>> --totalgray --ctab $FREESURFER_HOME/**FreeSurferColorLUT.txt --subject >>> bert >>> --brainmask mri/brainmask.mgz --brain-vol-from-seg >>> >>> I get the error that "SUBJECTS_DIR not defined in environment." My code >>> has >>> been edited to not even use this variable and yet the issue stills >>> stands. >>> Please advise on how to circumvent this error. >>> >>> Ever thankful, >>> Matthew Goldfinger >>> >>> >>> >> >> 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<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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SUBJECTS_DIR not defined in environment
by Matthew Goldfinger 30 Jul '12

30 Jul '12

Dear Freesurfers, Forgive me for asking about what appears to be a very simple issue but I am stumped. I have defined my SUBJECTS_DIR as evidenced by this output. ----- freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni But upon trying to execute the following: mri_segstats --seg /Applications/freesurfer/subjects/bert/mri/aseg.mgz --sum /Applications/freesurfer/subjects/bert/stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --subject bert --brainmask mri/brainmask.mgz --brain-vol-from-seg I get the error that "SUBJECTS_DIR not defined in environment." My code has been edited to not even use this variable and yet the issue stills stands. Please advise on how to circumvent this error. Ever thankful, Matthew Goldfinger

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Error with recon-all import step. ERROR: the pixel data cannot be loaded as it is JPEG compressed.
by Nathan Hutcheson 30 Jul '12

30 Jul '12

I am trying to import an MPRAGE structural sequence of 160 images acquired from a Siemens Allegro. Only one of my subjects displays the following error message when I try to import him using the "recon-all -s Subject -i" function. Below is the brief error message and full log. Thanks in advance for any assistance. *ERROR: the pixel data cannot be loaded as it is JPEG compressed.* Full Log Below: [Jill:freesurfer/subjects/RawDicoms] lab% recon-all -s SZ0069TS -i SZ0069TS/IM-0001-441581576-0001.dcm Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin Jill.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 /Applications/freesurfer/subjects/SZ0069TS \n mri_convert /Applications/freesurfer/subjects/RawDicoms/SZ0069TS/IM-0001-441581576-0001.dcm /Applications/freesurfer/subjects/SZ0069TS/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/RawDicoms/SZ0069TS/IM-0001-441581576-0001.dcm /Applications/freesurfer/subjects/SZ0069TS/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Applications/freesurfer/subjects/RawDicoms/SZ0069TS/IM-0001-441581576-0001.dcm... Getting Series No INFO: Found 163 files in /Applications/freesurfer/subjects/RawDicoms/SZ0069TS INFO: Scanning for Series Number 20 Scanning Directory INFO: found 160 files in series INFO: loading series header info. RunNo = 19 INFO: sorting. INFO: (256 256 160), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; *ERROR: the pixel data cannot be loaded as it is JPEG compressed.* (Transfer Syntax UID: 1.2.840.10008.1.2.4.70) Darwin Jill.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 recon-all -s SZ0069TS exited with ERRORS at Mon Jul 30 11:38:40 CDT 2012 For more details, see the log file /Applications/freesurfer/subjects/SZ0069TS/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Take care, Nathan Hutcheson Graduate Research Assistant 501 Sparks Center 1748 7th Ave South Birmingham, AL 35233

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