Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30086 discussions

Re: [Freesurfer] Converting an FSL label to Freesurfer space
by Douglas N Greve 29 Sep '10

29 Sep '10

The output has to be a volume (eg, nii or mgh), not a label. If you need a label, run mri_cor2label on the output. doug Massieh Moayedi wrote: > Hi Doug, > > I tried it, and it seems that it's working until the very last step. > > Here's the output I get: > > > $ mri_label2vol --seg > '/storage/AllUsers/Massih/FreeSurferData_TMD/SMA_Label_1mm_flipped.nii.gz' > --temp > '/storage/AllUsers/Massih/FreeSurferData_TMD/fsaverage/mri/orig.mgz' > --reg $FREESURFER_HOME/average/mni152.register.dat --invertmtx > --fillthresh 0.5 --o > /storage/AllUsers/Massih/FreeSurferData_TMD/SMA_Label_1mm_flipped_to_FS.label > > Number of labels: 0 > Annot File: (null) > Template Volume: > /storage/AllUsers/Massih/FreeSurferData_TMD/fsaverage/mri/orig.mgz > Outut Volume: > /storage/AllUsers/Massih/FreeSurferData_TMD/SMA_Label_1mm_flipped_to_FS.label > > Registration File: > /scratch/freesurfer_43/freesurfer/average/mni152.register.dat > Fill Threshold: 0.5 > Label Vox Vol: 1 > ProjType: (null) > ProjTypeId: 0 > ProjStart: 0 > ProjStop: 0 > ProjDelta: 0.1 > Subject: (null) > Hemi: (null) > UseNewASeg2Vol: 1 > DoLabelStatVol 0 > $Id: mri_label2vol.c,v 1.25.2.1 2008/12/19 23:18:26 greve Exp $ > Template RAS-to-Vox: -------- > -1.000 0.000 0.000 128.000; > -0.000 -0.000 -1.000 128.000; > -0.000 1.000 -0.000 128.000; > 0.000 0.000 0.000 1.000; > Template Voxel Volume: 1 > nHits Thresh: 0.5 > RegMat: -------- > 1.000 -0.004 -0.001 1.195; > 0.001 0.018 1.000 -19.147; > -0.004 -1.000 0.018 -16.617; > 0.000 0.000 0.000 1.000; > Inverting matrix > RegMat: -------- > 1.000 0.001 -0.004 -1.227; > -0.004 0.018 -1.000 -16.266; > -0.001 1.000 0.018 19.444; > 0.000 0.000 0.000 1.000; > Label RAS-to-Vox: -------- > -1.000 -0.001 0.004 129.227; > 0.001 -1.000 -0.018 108.556; > -0.004 0.018 -1.000 111.734; > 0.000 0.000 0.000 1.000; > ASeg2Vol: Building LUT > ASeg2Vol: Sorting > ASeg2Vol: Mapping > ASeg2Vol: Reverse Map > nmisses = 9558488 (2727 filled) > ASeg2Vol: done > unknown file type for file > (/storage/AllUsers/Massih/FreeSurferData_TMD/SMA_Label_1mm_flipped_to_FS.label) > > > Any ideas? > > Thanks, > Massih > On 09/29/2010 11:37 AM, Douglas N Greve wrote: >> I assume the label is a binary mask in MNI152? If so, use >> mri_label2vol and spec the label as a segmenation, use >> $FREESURFER_HOME/average/mni152.register.dat as the registration, >> specify --invertmtx, and use the orig.mgz in fsaverage as the >> template. I *think* this should work. >> >> doug >> >> mmoayedi wrote: >>> Hi everyone, >>> >>> I need to convert an FSL label (3D, MNI 152 space, 2mm brain) to >>> FreeSurfer's fsaverage brain inflated surface. >>> >>> Does anyone know how to do this? >>> >>> Thanks, >>> >>> Massih >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Changing and Saving Overlay Config in Tksurfer
by Adam Nitenson 29 Sep '10

29 Sep '10

Hi Freesurfers, I was wondering if there was a way to save any configurations you make to functional overlays (sig.mgh / sig.nii) in Tksurfer so you don't need to change them again. When I go to View --> Configure --> Overlay, it seems that the default is "Linear Opaque" with Min = 2.0 and Max = 5.0. For our purposes, I normally switch to "Piecewise" with Min = 1.3, Mid = 2.3, and Max = 3.3. It's an easy change to make normally, but I am having trouble loading these functional overlays into Slicer since it only loads the default settings with no way (as far as I know) to configure the overlay to display my preferences. Is there anyway I can permanently save these changes to a specific overlay so that it would load automatically that way, which will allow me to import it into other programs? I tried File --> Save Overlay As... after applying the changes, but it only saved the default config. Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

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Converting an FSL label to Freesurfer space
by mmoayedi 29 Sep '10

29 Sep '10

Hi everyone, I need to convert an FSL label (3D, MNI 152 space, 2mm brain) to FreeSurfer's fsaverage brain inflated surface. Does anyone know how to do this? Thanks, Massih

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white screen when opening freeview
by B.T. Thomas Yeo 29 Sep '10

29 Sep '10

Hi, when opening freeview while logged locally on a linux box (at Harvard NCF), we get a blank screen problem. See attached screenshot. Here, we have loaded multiple volumes in freeview, but in practice, we have this issue even when loading a single image. We are using stable4.5, and the linux version is: 2.6.18-194.3.1.e15 (redhat). An interesting thing is that when ssh-ing from a mac into the same linux box, we do not encounter such a problem. Thanks, Thomas

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mri_convert GradFile
by Steven Swinford 28 Sep '10

28 Sep '10

Hi FreeSurfer gurus, I'm trying to run a diffusion analysis on some old scans and am running into this error during mri_convert: ERROR: cannot open /usr/local/freesurfer/stable5/diffusion/mgh-dti-seqpack/gradient_mgh_dti06.gdt I noticed that stable4 has the GradFile with this naming convention, but stable5 only has a GradFile that omits the leading 0. usr/local/freesurfer/stable5/diffusion/mgh-dti-seqpack/gradient_mgh_dti6.gdt Are these the same GradFiles? Is there a way run these old scans through stable5 without this error? Thanks for your help, Steven

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Re: [Freesurfer] Space of FreeSurfer Stats
by Douglas N Greve 28 Sep '10

28 Sep '10

Hi Tyler, I'm not sure what you mean by the stats being in a particular space. I had understood it to mean the space that volumes would be measured in. Is that right? If so, then the volumes will be measured in the space of the input, whatever input you supplied. doug ps. I'm copying the freesurfer list here so that others may benefit from the answer and so that the answer (not just the question) are searchable in are archive. blazey(a)artsci.wustl.edu wrote: > Hi Doug, > > Thank you for your quick response. I realize now, however, that my > question didn't quite get at what I was asking. What I meant to ask was > whether or not the stats outputted by FreeSurfer are in input space, not > whether they were in native space per se. So if I were register a session > to an atlas before putting it through FreeSurfer, would FreeSurfer output > stats in my atlas space? Sorry for my mistake and thanks again. > > - Tyler > > >> yes, they are measured in native space. >> >> doug >> >> blazey(a)artsci.wustl.edu wrote: >> >>> Hi All, >>> >>> Are the volume stats outputted by FreeSurfer in native space or in >>> FreeSurfer's space? According to some older mailing list questions, they >>> are in native space, but I wanted to make sure that this was still the >>> case. Thanks in advance for any help. >>> >>> - Tyler >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> >> >> 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. >> >> > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Space of FreeSurfer Stats
by blazey＠artsci.wustl.edu 28 Sep '10

28 Sep '10

Hi All, Are the volume stats outputted by FreeSurfer in native space or in FreeSurfer's space? According to some older mailing list questions, they are in native space, but I wanted to make sure that this was still the case. Thanks in advance for any help. - Tyler

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error in recon-all -autorecon3
by Paola Valsasina 28 Sep '10

28 Sep '10

Dear FS list, I am trying to finish my first analyses with freesurfer; however, I have some problems when running the last stages of recon-all. In summary what I did: 1) recon-all -autorecon1 (worked well) 2) some minor brain strip editing 3) recon-all -autorecon2 (worked well) 4) some editing both of white matter and adding some control points 5) Now I have run recon-all -autorecon2-cp -autorecon3, but I receive the following error (after many hours of post-processing): mris_volmask -label_left_white 2 -label_left_ribbon 3 -label_right_white 41 -label_right_ribbon 42 -save_ribbon -save_distance "subject_name" mris_volmask.bin: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory recon-all exited with errors Apparently, cortical segmentation has been performed, since I see in the stats folder both ?h.aparc.stats and ?h.aparc.a2009s.stats files. Which additional output am I missing because of this error? Thank you for your help Paola Paola Valsasina Research Fellow to Prof. M. Filippi Neuroimaging Research Unit Institute of Experimental Neurology Hospital San Raffaele via Olgettina 60 20132 Milan - ITALY

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Re: [Freesurfer] Freesurfer Digest, Vol 79, Issue 32
by Siti Hajar 28 Sep '10

28 Sep '10

When I ran this command, " mri_segstats --seg "$fsaveragesurfpath"/"$hemi".fsaverage."$hemi"_"$roi"_"$subj".mgh --in "$hemi".thickness.fsaverage.mgh --sum segstats-"$hemi"_"$roi"_"$subj".txt, this kind of output came out "mghRead(/usr/local/freesurfer/subjects/100905lsy/surf/lh.thickness.fsaverage.mgh, -1): could not open file--> which indicated that there was no lh.thickness.fsaverage.mgh created. Well, basically, when I ran recon-all, lh.thickness.fsaverage.mgh should be created, but it wasn't. So, again with my question,is this situation happened due to the new freesurfer software that I installed or was it caused by other source? Thank you ________________________________ From: "freesurfer-request(a)nmr.mgh.harvard.edu" <freesurfer-request(a)nmr.mgh.harvard.edu> To: freesurfer(a)nmr.mgh.harvard.edu Sent: Mon, September 20, 2010 9:49:16 PM Subject: Freesurfer Digest, Vol 79, Issue 32 Send Freesurfer mailing list submissions to freesurfer(a)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(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)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. Re: mri_label2volume issues (Michael Waskom) 2. Generating a 'non-zero' group mask (Marco Loggia, PhD) 3. Re: recon-all quality control checks on large numbers of subjects (Nick Schmansky) 4. lh.thickness.fsaverage (Siti Hajar) 5. Re: lh.thickness.fsaverage (Douglas Greve) ---------------------------------------------------------------------- Message: 1 Date: Fri, 17 Sep 2010 11:04:00 -0400 From: Michael Waskom <mwaskom(a)mit.edu> Subject: Re: [Freesurfer] mri_label2volume issues To: Freesurfer(a)nmr.mgh.harvard.edu Message-ID: <AANLkTi=5ZnihXybQu0Wwf-ysJN6oPoQk2bFuf2_iirzb(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Prapti, Basically, you just need to have a label file that you can turn into a lh.your_annot_name.annot (assuming your actual ROI is in the right hemisphere), so that mri_label2annot runs properly. The easiest thing to do would be to rename any old label you have in your subject's label directory to lh.dummy.label, and then create an annotation from that label with mri_label2annot. Then run mris_aparc2aseg as you tried to do before, which will create a volume that has 0's everywhere except in the area where your actual and dummy labels were projected. Figure out the voxel values for the ROI you want (using Freeview or tkmedit), and then run: mri_binarize --i your_annot_name+aseg.mgz --match <that voxel value> --o you_roi_name.mgz Which will have 1s where your ROI is and 0s everywhere else. Best, Mike -------Original Message------- Hi Doug, Thanks for the reply. I am sorry, I am a bit confused about what you mean by creating a dummy label. I am also not sure at which step I need to do this. As I understand it, I use mri_label2annot to transform my label into a annotation file and this will be separate for the two hemispheres. Do I then edit these files ? where exactly do I use mri_binarize? Thanks, Prapti -----Original Message----- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Friday, 17 September 2010 12:44 AM To: Prapti Gautam Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2volume issues Right, I see, mri_aparc2aseg is hard-coded to expect both lh and rh. The easiest thing is to make a dummy label for the other hemisphere. In the final segmentation, left hemisphere will have an index of 1000+something, the right will have 2000+something. You can then use mri_binarize with --match create a new binary volume with just your hemisphere. doug Prapti Gautam wrote: > Hi Doug, > > Thanks for the reply. I have tried using the method you've suggested, > however, I'm stuck because mri_label2annot which I use to turn my label > into a annot file only works in one hemisphere while mri_aparc2aseg > works for the whole brain. Do you know a work around for this? > > Can I merge the annot files created from each hemisphere so that I can > pass it to mri_aparc2aseg? > > > Thanks, > > Prapti > > > ------------------------------ Message: 2 Date: Fri, 17 Sep 2010 11:38:22 -0400 From: "Marco Loggia, PhD" <marco(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Generating a 'non-zero' group mask To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <5EA6CF4FA3914BC49D4CC51BD03A8618@MARCOWORK> Content-Type: text/plain; charset="us-ascii" Dear all, I am performing surface analyses on ASL CBF maps. As these maps do not cover the whole brain, and some masks have larger brain coverage than others, I would need to create a binary surface mask (in the fsaverage space) which would zero out the vertices where at least one of my subjects have a zero value. This map would then be used to spatially limit my statistical analyses in mri_glmfit. Any suggestions? Thanks a lot, Marco _____________________ Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School CNY Building 120, suite 101E Charlestown, Massachusetts 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 marco(a)nmr.mgh.harvard.edu

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Pial Edit on Atrophied Brain
by Soon Hock Wei 27 Sep '10

27 Sep '10

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