Freesurfer October 2013

freesurfer@nmr.mgh.harvard.edu

136 participants
244 discussions

R: Re: R: Re: analysis on 4-6yrs pat
by crailo＠inwind.it 25 Oct '13

25 Oct '13

Hi Bruce, I guess running from scratch is the easiest way. I tried to upload the whole dir but it seems I cannot have access to it. Thanks Regards Antonio >----Messaggio originale---- >Da: fischl(a)nmr.mgh.harvard.edu >Data: 25/10/2013 15.33 >A: "crailo(a)inwind.it"<crailo(a)inwind.it> >Cc: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: analysis on 4-6yrs pat > >Hi Antonio > >I need the whole subject directory to diagnose what happened with the FS >analysis. Or I can try rerunning it from scratch here instead if you >prefer >Bruce >On Fri, 25 Oct 2013, crailo(a)inwind.it wrote: > >> Hi Bruce, >> thanks for the reply. I have uploaded two images, the original one and the one >> preprocessed via 3D slicer N3. >> Thanks >> Regards >> Antonio >> >>> ----Messaggio originale---- >>> Da: fischl(a)nmr.mgh.harvard.edu >>> Data: 25/10/2013 14.07 >>> A: "crailo(a)inwind.it"<crailo(a)inwind.it> >>> Cc: <freesurfer(a)nmr.mgh.harvard.edu> >>> Ogg: Re: [Freesurfer] analysis on 4-6yrs pat >>> >>> Hi Antonio >>> >>> it's tough to diagnose from one slice. Is the top of the head in general >>> darker than the bottom? It looks like it, but that might also be lower >>> myelin content. If you upload the subject we'll take a look. >>> >>> cheers >>> Bruce >>> On Fri, 25 Oct >>> 2013, crailo(a)inwind.it wrote: >>> >>>> >>>> Dear Freesurfer experts, >>>> >>>> I am trying to run cortical thickness analysis on 4-6 yrs old patients but >> I >>>> have some problem to get nice cortical gray matter. I have tried to run >>>> several N3 but with no success so I would need to ask whether you could >> give >>>> me hints to improve that. Please find attached a screenshot of what I do >>>> get. >>>> >>>> >>>> Many thanks for any help. >>>> >>>> >>>> Best Wishes >>>> >>>> Antonio >>>> >>>> >>>> >>> >>> >>> 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. >>> >>> >> >> >> >> >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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asegstats2table error
by Rashmi Singh 25 Oct '13

25 Oct '13

Hello, This morning I tried to get the segmentation measurement in table formate, but I got the following error message asegstats2table --subjects AB197.T0b AB232.T0a AD721.T0 --skip --meas volume --tablefile asegstats1.txt Error message :SUBJECTS_DIR : /opt/freesurfer/subjects Parsing the .stats files Skipping /opt/freesurfer/subjects/AB197.T0b/stats/aseg.stats Skipping /opt/freesurfer/subjects/AB232.T0a/stats/aseg.stats Skipping /opt/freesurfer/subjects/AD721.T0/stats/aseg.stats Building the table.. Traceback (most recent call last): File "/opt/freesurfer/bin/asegstats2table", line 513, in <module> rows, columns, table = sanitize_table(options, pretable) File "/opt/freesurfer/bin/asegstats2table", line 412, in sanitize_table _specs, _id_name_map, _measl = _t[0] IndexError: list index out of range Then tried asegstat2table for individual subjects but for each subject the computer gave following error message Example: asegstats2table --subjects AB232.T0a --meas volume --tablefile asegstats1.txt SUBJECTS_DIR : /opt/freesurfer/subjects Parsing the .stats files ERROR: The stats file /opt/freesurfer/subjects/AB232.T0a/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files I looked into each subjects' segmetation file (attached). It looked fine to me and had all the information. Please advise why I got error message. Thanks, Rashmi

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Question about freesurfer coordinates
by Leila Reddy 25 Oct '13

25 Oct '13

Hi, I've been trying to understand the FScoordinates powerpoint and I would like to ask a few questions (these questions might simply be about mri_convert, depending on where my confusion is...). 1) I think the orig.mgz volume is in the CRS space. Now, looking at slide 8 in the powerpoint, if I want to go from a point in orig.mgz (CRS) to the corresponding point in MNI305 (CRS), I would have to do: inv(Nb)*X*Na*my_point. However, to get the whole volume from orig.mgz to MNI305, the following command does the job: mri_convert orig.mgz --apply_transform transforms/talariach.xfm -oc 0 0 0 orig.talairach.mgz. Does this step automatically include the Na and inv(Nb) operations? Or am I wrong about the starting spaces for orig.mgz and MNI305? 2) I get the same result as above for the talairach transform if I use: mri_convert --apply_transform transforms/talariach.xfm --devolvexfm subjectid -ic 0 0 0 orig talairach. I see now what devolvexfm is, but which space in the flowchart on slide 8 is it operating on? -ic and -oc seem to be important because I don't get the same results if I use -ic for the first command and -oc for the second command, but I don't find any documentation on what exactly these options do. Thanks, Leila

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R: Re: analysis on 4-6yrs pat
by crailo＠inwind.it 25 Oct '13

25 Oct '13

Hi Bruce, thanks for the reply. I have uploaded two images, the original one and the one preprocessed via 3D slicer N3. Thanks Regards Antonio >----Messaggio originale---- >Da: fischl(a)nmr.mgh.harvard.edu >Data: 25/10/2013 14.07 >A: "crailo(a)inwind.it"<crailo(a)inwind.it> >Cc: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] analysis on 4-6yrs pat > >Hi Antonio > >it's tough to diagnose from one slice. Is the top of the head in general >darker than the bottom? It looks like it, but that might also be lower >myelin content. If you upload the subject we'll take a look. > >cheers >Bruce >On Fri, 25 Oct >2013, crailo(a)inwind.it wrote: > >> >> Dear Freesurfer experts, >> >> I am trying to run cortical thickness analysis on 4-6 yrs old patients but I >> have some problem to get nice cortical gray matter. I have tried to run >> several N3 but with no success so I would need to ask whether you could give >> me hints to improve that. Please find attached a screenshot of what I do >> get. >> >> >> Many thanks for any help. >> >> >> Best Wishes >> >> Antonio >> >> >> > > >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. > >

2 1

analysis on 4-6yrs pat
by crailo＠inwind.it 25 Oct '13

25 Oct '13

Dear Freesurfer experts, I am trying to run cortical thickness analysis on 4-6 yrs old patients but I have some problem to get nice cortical gray matter. I have tried to run several N3 but with no success so I would need to ask whether you could give me hints to improve that. Please find attached a screenshot of what I do get. Many thanks for any help. Best Wishes Antonio

2 1

Incorrect orientations from MRI convert
by Chiu, Bryan (PHTH) 24 Oct '13

24 Oct '13

Hi, I am working on a dataset using free surfer. I have NIFTII files which I am converting using mri_convert. Upon completion of mri_convert, the orientations of the files are wrong. This likely leads to an incorrect talairach (I was getting errors but used -notal-check) and leads to an incorrect labelling of volumes from the -autorecon-all. My sagittal view is rotated 90 degrees clockwise on the MRI convert. The sagittal and coronal views are swapped. This appears in a tkmedit of the converted file. error codes during mri_convert are as follows: $ mri_convert '/Applications/freesurfer/subjects/001test/xxxxx-file-xxxxxx.nii.gz' '/Applications/freesurfer/subjects/001test/''orig2.mgz' mri_convert /Applications/freesurfer/subjects/001test/xxxxx-file-xxxxxx.nii.gz.nii.gz /Applications/freesurfer/subjects/001test/orig2.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Applications/freesurfer/subjects/001test/HANDY_POWER_001_10_1_NIFTI.nii.gz... WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 WARNING: it does not appear that there was sufficient information in the input to assign orientation to the volume... i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /Applications/freesurfer/subjects/001test/orig2.mgz guidance to fix this would be appreciated. - Bryan

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problem with freesurfer installation/tkmedit
by Elissa McIntosh 24 Oct '13

24 Oct '13

Hi, I think there is a problem with my freesurfer installation (newest version 5.3). First, when trying this freeview command (see below) I found on the “Testing your freesurfer installation” page using my own data, freesurfer opened, but I am concerned about the “invalid drawable” lines. The message happened when I ran this command on the "bert" data. [CoS-Psychology-Murphy-iMac-QAD:/Applications/freesurfer] cmurphy% freeview -v $SUBJECTS_DIR/ABU/mri/norm.mgz -v $SUBJECTS_DIR/ABU/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS_DIR/ABU/surf/lh.white:edgecolor=yellow -f $SUBJECTS_DIR/ABU/surf/rh.white:edgecolor=yellow -f $SUBJECTS_DIR/ABU/surf/lh.pial:annot=aparc:edgecolor=red -f $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red 2013-10-22 12:47:02.811 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.812 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.826 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.826 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.839 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.840 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.853 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.853 Freeview[4214:703] invalid drawable reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) MRISread(/Applications/freesurfer/elissa_thesis/bert/surf/rh.pial): could not open file No such file or directory MRISread failed MRISread(/Applications/freesurfer/elissa_thesis/bert/surf/rh.pial): could not open file rfer/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) CTABisEntryValid: index -1 was OOB No such file or directory CTABisEntryValid: index -1 was OOB No such file or directory CTABisEntryValid: index -1 was OOB iginally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) CTABisEntryValid: index -1 was OOB No such file or directory CTABisEntryValid: index -1 was OOB No such file or directory CTABisEntryValid: index -1 was OOB No such file or directory CTABisEntryValid: index -1 was OOB No such file or directory CTABisEntryValid: index -1 was OOB iginally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Second, my next issue is that I am unable to use tkmedit to view my data. See command below and error message. [CoS-Psychology-Murphy-iMac-QAD:/Applications/freesurfer] cmurphy% tkmedit ABU orig.mgz dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer/tktools/tkmedit.bin Reason: image not found Trace/BPT trap I've tried other tkmedit commands and have gotten same error messages. I tried commands on "bert" data but got same errors. Third, I'd like to know if it is normal that a recon all could only take between 8-9 hours. I have attached the recon-all.log for the subject I am trying to view. Here is some additional information about my mac incase you see any glaring system inadequacies. Processor 2.5 GHz Intel Core i5 Memory 4 GB 1333 MHz DDR3 Graphics AMD Radeon HD 6750M 512 MB Software Mac OS X Lion 10.7.5 (11G63) Thank you, Elissa

2 1

Total WM volume
by Fotiadis, Panagiotis 24 Oct '13

24 Oct '13

Hi FS Community, Does the "Total cortical white matter volume" parameter in the aseg.stats file represent the total wm volume in the brain? Thank you in advance, Panos

1 0

How do you create labels from binary masks?
by Marcos Martins da Silva 24 Oct '13

24 Oct '13

Hi, Freesurfers. I need to create some labels from binary masks. Sometime ago I read a post (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-October/033783.… ) and, unless I am wrong, it seemed to me that mri_label2vol could be the tool to get it. If so, could you please explain how? I read documentation on wiki and help from the command itself and could not see how to accomplish that. I could only find how to create a volume from a label. What I need to do is to get a mask like the binLeftHippoHead.mgz (attached) and create a label. Assuming it is possible, I could also make labels for Hippocampal body and head, merge the 3 labels into an annot file. This way i can use Freeview to load the whole hippocampal surface and discriminate the 3 segments by colors with the annot file. Thanks in advance for any help. Cheers, Marcos.

3 5

Extracting individuals data at a vertex
by O'Shea,Andrew 24 Oct '13

24 Oct '13

Hello FS experts, In QDEC when I click on a vertex a scatter plot is generated with each individuals data for that vertex. Is there a simple way to extract that data (for each subject) into spreadsheet form for a specific vertex? -Andrew

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Freesurfer October 2013