Freesurfer

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30132 discussions

Re: [Freesurfer] installation trouble - error message subjects directory not recognised
by Z K 28 Oct '13

28 Oct '13

Sven, Well that certainly is odd that. My guess is that there is some sort of extension that Mac is hiding in the finder window (along the lines of what you were talking about with the text editor). Im also a little concerned about the double '//' that is part of your FREESURFER_HOME environment variable. That should not be there, although I don't think its necessarily a problem. Please open a terminal and type the following command: 'touch /Applications/freesurfer/.license' That should fix your problem. Let me know if not. Also, please CC the list on these responses so that they can be stored for others to view. -Zeke On 10/24/2013 02:29 PM, muellersvenc wrote: > Hi Zeke, > > the output in both cases is: "no such file or directory". I have attached a screenshot to this email and you can see my freesurfer directory and the .license file at the very top. Is this maybe a problem with creating such a file with the text editor? There is also a file called LICENSE in the directory but this just contains the license agreement. > > I really appreciate you helping me as I am keen on getting freesurfer to work. So, thank you so much for your time and effort in helping me through this! Much appreciated! > > Sven > > > > > > On 24-okt-2013, at 17:35, Z K wrote: > >> If there really is a .license in the FREESURFER_HOME directory then everything should be working fine. What is the output when you type: >> >> 'ls -l /Applications/freesurfer/.license' >> >> at the command line? And what is the output when you type: >> >> 'ls -l $FREESURFER_HOME/.license' >> >> >> On 10/24/2013 11:25 AM, muellersvenc wrote: >>> Hi Zeke, >>> >>> that seems to have worked (strangely because I didn't really do anything different before other than a fresh reinstall). >>> >>> However, now I have problems with the license file when trying to test the installation as suggested on the "Testing your freesurfer installation" webpage. >>> >>> I did a fresh installation, then created a ".license" file using the text editor containing the three lines that were sent to me by email and placed this file into the freesurfer folder which is my FREESURFER_HOME (/Applications/freesurfer). Then I did the sourcing. And then when I type for instance >>> >>> [pp05c332:/Applications] switch% tkmedit bert orig.mgz >>> -------------------------------------------------------------------------- >>> ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. >>> If you are outside the NMR-Martinos Center, >>> go to http://surfer.nmr.mgh.harvard.edu to >>> get a valid license file (it's free). >>> If you are inside the NMR-Martinos Center, >>> make sure to source the standard environment. >>> -------------------------------------------------------------------------- >>> [pp05c332:/Applications] switch% >>> >>> >>> Any ideas what I am doing wrong? I changed the settings on my computer a while ago and I can see the hidden files so can also see that there is a file called ".license" in the freesurfer folder but am not sure why freesurfer is not recognising it. >>> >>> Many thanks in advance for your help! >>> >>> sven >>> >>> >>> >>> On 24-okt-2013, at 16:39, Z K wrote: >>> >>>> Hi Sven, >>>> >>>> Whats most likely happening is that you are defining SUBJECTS_DIR prior to sourcing SetUpFreeSurfer.csh. Freesurfer will not overwrite the SUBJECTS_DIR environment variable if it already exists at the time of sourcing the SetUpFreeSurfer.csh. This is most likely occuring in your .cshrc file. >>>> >>>> To verify, type 'echo $SUBJECTS_DIR' before sourcing and see what the output says. >>>> >>>> -Zeke >>>> >>>> On 10/24/2013 09:10 AM, muellersvenc wrote: >>>>> Hi all, >>>>> >>>>> I am running into trouble testing my freesurfer installation on a Mac (10.6.8). I followed all steps in the guide but there is something funny that freesurfer does not seem to recognise its own "subjects" directory (see attached screenshot). If screenshot is not visible, it says: >>>>> >>>>> -------- freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 -------- >>>>> Setting up environment for FreeSurfer/FS-FAST (and FSL) >>>>> WARNING: Applications/freesurfer/subjects does not exist >>>>> FREESURFER_HOME /Applications/freesurfer >>>>> FSFAST_HOME /Applications/freesurfer/fsfast >>>>> FSF_OUTPUT_FORMAT nii.gz >>>>> SUBJECTS_DIR Applications/freesurfer/subjects >>>>> MNI_DIR /Applications/freesurfer/mni >>>>> FSL_DIR /usr/local/fsl >>>>> >>>>> I think it might have to do with the fact that there is a "/" missing in front of the "Applications" but I don't know where/how to change this. I checked my StartUp.csh file and there everything seems fine. However, the subjects directory was definitely created by freesurfer (also screenshot) so there is a mismatch somewhere. >>>>> >>>>> I am sure it is a simple thing but can someone please let me know what I should do so I can start to enjoy freesurfer? >>>>> >>>>> Many thanks in advance, >>>>> >>>>> sven >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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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Power of MRI machine
by Muhammad Naveed Iqbal Qureshi 28 Oct '13

28 Oct '13

Dear Community, Is it possible to detect the scanning power (either 1.5 or 3 tesla) of MRI acquisition machine from the dicom images, if we do not know about the scanner properties? Best Regards, Muhammad Naveed Iqbal Qureshi

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Re: [Freesurfer] Incorrect orientations from MRI convert
by Chiu, Bryan (PHTH) 27 Oct '13

27 Oct '13

Hi Douglas, I've looked at the original images in freeview and they follow the correct talairach coordinates. I've run mri_convert again and the files follow the correct talairach coordinates. It appears this may have been a 'one-off' issue. Will update after I autorecon everything. - Bryan

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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. > >

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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

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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

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