Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30091 discussions

FW: Freesurfer fails
by Franklin, Crystal G 14 Jan '13

14 Jan '13

On 1/14/13 11:38 AM, "Franklin, Crystal G" <FRANKLINC(a)uthscsa.edu> wrote: >I put the data on your ftp site in the folder called >crystal_failed_talairach.tar. > >Thanks, >Crystal > >On 1/14/13 9:31 AM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: > >>Hi Crystal >> >>we'll need the image volume also >> >>cheers >>Bruce >>On Mon, 14 Jan 2013, Franklin, Crystal G >>wrote: >> >>> Bruce, >>> >>> I have visually checked the transforms and they do indeed seem >>>incorrect. >>> The images are stretched. I have attached the talairach.xfm for one of >>> the images that failed and one that worked. >>> >>> Thanks for all your help, >>> Crystal >>> >>> On 1/13/13 3:08 PM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: >>> >>>> can you cc the list? Have you visualized the transform to see if it is >>>> indeed incorrect? >>>> >>>> On Sun, 13 Jan 2013, Franklin, Crystal G wrote: >>>> >>>>> I used mri_convert to create the 001.mgz file. In freeview the >>>>> directions appear correct. >>>>> >>>>> Thanks, >>>>> Crystal >>>>> -----Original Message----- >>>>> From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>>>> Date: Sun, 13 Jan 2013 09:02:16 >>>>> To: Franklin, Crystal G<FRANKLINC(a)uthscsa.edu> >>>>> Cc: Freesurfer(a)nmr.mgh.harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >>>>> Subject: Re: [Freesurfer] Freesurfer fails >>>>> >>>>> Hi Crystal >>>>> >>>>> how did you create the 001.mgz? When you view it in freeview does >>>>> freeview have the correct directions in the anatomy (i.e. I/S, A/P >>>>>and >>>>> L/R)? >>>>> >>>>> cheers >>>>> Bruce >>>>> On Sat, 12 Jan 2013, Franklin, Crystal G wrote: >>>>> >>>>>> Freesurfer, >>>>>> >>>>>> I have been running a group of subjects through recon-all and some >>>>>>of >>>>>> the >>>>>> subjects are failing at the very beginning of the process and I am >>>>>>not >>>>>> sure >>>>>> why. The images look fine, but I keep getting the following >>>>>>error: >>>>>> >>>>>> #@# Talairach Failure Detection Fri Dec 7 10:54:57 CST 2012 >>>>>> /Applications/freesurfer/subjects/PHY002/mri >>>>>> \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n >>>>>> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm >>>>>> ***FAILED*** (p=0.0013, pval=0.0000 < threshold=0.0050) >>>>>> INFO: Attempting MINC mritotal to perform Talairach align >>>>>> >>>>>> Do you know what could be causing this? >>>>>> >>>>>> I read that you can include the command ?notal ?check to skip this >>>>>> test, but how >>>>>> will this effect my data? If I run this command on the subjects >>>>>>that >>>>>> failed and combine their results with the subjects that worked will >>>>>>my >>>>>> group >>>>>> results be effected? >>>>>> >>>>>> Any help would be appreciated. I have attached one of the log files >>>>>> for a >>>>>> subject that failed. >>>>>> >>>>>> Thanks, >>>>>> Crystal >>>>>> >>>>>> >>>>> >>>>> >>>>> 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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Fwd: Problems in testing out newly installed Freesurfer with autorecon-1 option
by Susan Kuo 14 Jan '13

14 Jan '13

Thank you, Nick. I tried using fixup_mni_paths, but received a poor result. I copied the stdout below: *** yocto/j/dti7/Susie/freesurfer/subjects> su Password: root@yocto:/j/dti7/Susie/freesurfer/subjects# fixup_mni_paths fixup_mni_paths: command not found root@yocto:/j/dti7/Susie/freesurfer/subjects# cd $FREESURFER_HOME/bin root@yocto:/usr/local/freesurfer/bin# fixup_mni_paths fixup_mni_paths: command not found root@yocto:/usr/local/freesurfer/bin# ./fixup_mni_paths Using perl '/usr/bin/perl' Patching autocrop...(original file saved to autocrop.old) Patching field2imp...(original file saved to field2imp.old) Patching imp2field...(original file saved to imp2field.old) Patching make_template...(original file saved to make_template.old) Patching mritoself...(original file saved to mritoself.old) Patching mritotal...(original file saved to mritotal.old) Patching nu_correct...(original file saved to nu_correct.old) Patching nu_estimate...(original file saved to nu_estimate.old) Patching nu_estimate_np_and_em...(original file saved to nu_estimate_np_and_em.old) Patching nu_evaluate...(original file saved to nu_evaluate.old) Patching resample_labels...(original file saved to resample_labels.old) Patching sharpen_volume...(original file saved to sharpen_volume.old) Patching xfmtool...(original file saved to xfmtool.old) done. Here are the changes: diff autocrop autocrop.old diff field2imp field2imp.old diff imp2field imp2field.old diff make_template make_template.old diff mritoself mritoself.old diff mritotal mritotal.old diff nu_correct nu_correct.old diff nu_estimate nu_estimate.old diff nu_estimate_np_and_em nu_estimate_np_and_em.old diff nu_evaluate nu_evaluate.old diff resample_labels resample_labels.old diff sharpen_volume sharpen_volume.old diff xfmtool xfmtool.old done. Note: not all systems will require a patch, and may not show any differences. Now a test of the MNI tool 'nu_correct'... nu_correct: Command not found. A version number and usage message should have been displayed. *** I double-checked that /usr/bin/perl exists, so that's ok. I've been crawling the forums, but I can't find a good answer for what appears to be a simple problem. Can I fix this manually? Thanks! Susie On Wed, Jan 9, 2013 at 4:29 PM, Nick Schmansky <nicks(a)nmr.mgh.harvard.edu>wrote: > Susan, > > there appear to be two problems here. the first and main problem is the > one: > > nu_correct: Command not found. > > nu_correct is a script which has as its first line: > > #!/usr/bin/perl -w > > so can you check that you have perl installed at /usr/bin/perl? > > better yet, run this script: > > fixup_mni_paths > > which does the checking for you and attempts to fix the scripts. > > the other problem appears to be the fact that mri_nu_correct.mni doesnt > exit upon finding the error that the files are missing. this is bad, > although in looking at the script, it ought to. the next release will > contain a double check. from the looks of your script, it appears that > you are running recon-all with a subject that had its data already > processed, so nu.mgz existed already, so it just used that and continued > on. so the results are correct (assuming nu.mgz was decent to begin > with), but resolving the nu_correct issue is the important thing to do. > > Nick > > > On Wed, 2013-01-09 at 11:00 -0500, Susan Kuo wrote: > > Hi, > > I'm currently in the process of verifying that my install of > > Freesurfer works. I have an Ubuntu 12.04.1 LTS box. I encountered what > > appeared to be 4 errors after running recon-all -s bert -autorecon1. > > The last line I included here states that the command completed > > without error, so I'm not sure if I should be concerned > > thatnu_correct wasn't found, or that there were loading errors, and > > a mincREAD() error. Could you help me identify what I need to do to > > correct these issues? I've included the standard output for this > > command as a text file here. There appear to be 4 issues: > > > > > > > > > > ***ISSUE 1: cannot find nu_correct ************************* > > nu_correct: Command not found. > > INFO: current FREESURFER_HOME does not match that of previous > > processing. > > > > > > ***ISSUE 2: No such file or directory error******************** > > cp: cannot stat `./tmp.mri_nu_correct.mni.25253/nu2.mnc': No such file > > or directory > > mri_binarize --i ./tmp.mri_nu_correct.mni.25253/nu2.mnc --min -1 > > --o ./tmp.mri_nu_correct.mni.25253/ones.mgz > > mincRead(): can't find file ./tmp.mri_nu_correct.mni.25253/nu2.mnc > > > > > > ***ISSUE 3: Loading error****************************** > > Loading ./tmp.mri_nu_correct.mni.25253/ones.mgz > > ERROR: loading ./tmp.mri_nu_correct.mni.25253/ones.mgz > > mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.25253/ones.mgz > > --i ./tmp.mri_nu_correct.mni.25253/nu2.mnc > > --sum ./tmp.mri_nu_correct.mni.25253/sum.junk > > --avgwf ./tmp.mri_nu_correct.mni.25253/output.mean.dat > > mghRead(./tmp.mri_nu_correct.mni.25253/ones.mgz, -1): could not open > > file > > > > > > ***ISSUE 4: Loading error****************************** > > Loading ./tmp.mri_nu_correct.mni.25253/ones.mgz > > ERROR: loading ./tmp.mri_nu_correct.mni.25253/ones.mgz > > (standard_in) 1: syntax error > > mris_calc > > -o ./tmp.mri_nu_correct.mni.25253/nu2.mnc > ./tmp.mri_nu_correct.mni.25253/nu2.mnc mul > > mincRead(): can't find file ./tmp.mri_nu_correct.mni.25253/nu2.mnc > > > > > > ****This is the last line to standard output, and it seems > > reassuring********************** > > recon-all -s bert finished without error at Tue Jan 8 17:49:19 EST > > 2013 > > > > > > > > > > I appreciate whatever help you can give me, and thank you very much > > for your time! The attached is a text file. > > > > > > > > > > Best, > > S Kuo > > _______________________________________________ > > 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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Tracula problems initializing pathway
by Cat Chong 14 Jan '13

14 Jan '13

Hello Experts I am still at the first pre-proc step for Tracula and although the script is running, it seems to have difficulty initializing the first pathway (1 out of 18) Please see below script excerpt: Is that normal that it takes this many trials to initiate a pathway? Cheers, Catherine WARN: Could not find satisfactory control point fit - try 171 Finding center streamline INFO: Step is 5 voxels WARN: Turning off FA check for center streamline INFO: Step is 5 voxels INFO: Length of center streamline is 111 voxels Selecting 5 points on center streamline INFO: Step is 4 voxels WARN: Defaulting to equidistant control points INFO: Selected control points are 96 100 30 106 108 58 116 109 87 113 102 115 108 105 146 INFO: Distances between consecutive points are 31 31 29 32 WARN: Could not find satisfactory control point fit - try 172 Finding center streamline INFO: Step is 5 voxels WARN: Turning off FA check for center streamline INFO: Step is 5 voxels INFO: Length of center streamline is 107 voxels Selecting 5 points on center streamline INFO: Step is 4 voxels

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Re: [Freesurfer] Tracula error? set: Variable name must begin with a letter
by Anastasia Yendiki 14 Jan '13

14 Jan '13

Great, glad it works! On Mon, 14 Jan 2013, Cat Chong wrote: > Dear Anastasia, > > Thank you so much for your fast reply. I believe I found the pesky mistake > in my dmrirc file.. I omitted a space > in the last line > set ncpts =5 > once I fixed this to set ncpts = 5 and re-ran the command I no longer get > this error message. > Thank you very much, > Catherine > > > > ____________________________________________________________________________ > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > To: Cat Chong <cavecreekcutter(a)yahoo.com> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Monday, January 14, 2013 10:04 AM > Subject: Re: [Freesurfer] Tracula error? set: Variable name must begin with > a letter > > > Hi Cat - Can you please send along your dmrirc file? It's hard to tell > without looking at it. > > a.y > > On Mon, 14 Jan 2013, Cat Chong wrote: > > > > > Hello Experts: > > > > I am running the first pre-processing step in Tracula and come across the > > error: > > set: Variable name must begin with a letter. > > > > Below is an excerpt of the script which seems to be running fine. Did I > make > > a mistake in my > > dmrirc_single_subject file? > > Cheers, > > Catherine > > > > fmris-mac-pro-2:8000_tracula fmri$ trac-all -prep -c > > $SUBJECTS_DIR/dmrirc_single_subject > > set: Variable name must begin with a letter. > > INFO: SUBJECTS_DIR is /8000_tracula/ > > INFO: Diffusion root is /8000_tracula//8000_tracula_out/ > > Actual FREESURFER_HOME /Applications/freesurfer > > trac-preproc -c > > /8000_tracula//8000_tracula_out//8001_DTI/scripts/dmrirc.local -log > > /8000_tracula//8000_tracula_out//8001_DTI/scripts/trac-all.log -cmd > > /8000_tracula//8000_tracula_out//8001_DTI/scripts/trac-all.cmd > > #------------------------------------- > > /Applications/freesurfer//bin/trac-preproc > > #------------------------------------- > > #@# Image corrections Mon Jan 14 09:37:29 MST 2013 > > mri_convert /8000_tracula//8001_DTI/IM-0006-0001.dcm > > /8000_tracula//8000_tracula_out//8001_DTI/dmri/dwi_orig.nii.gz > > mri_convert /8000_tracula//8001_DTI/IM-0006-0001.dcm > > /8000_tracula//8000_tracula_out//8001_DTI/dmri/dwi_orig.nii.gz > > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > > reading from /8000_tracula//8001_DTI/IM-0006-0001.dcm... > > Starting DICOMRead2() > > dcmfile = /8000_tracula//8001_DTI/IM-0006-0001.dcm > > dcmdir = /8000_tracula//8001_DTI > > Ref Series No = 6 > > > > > > the script continues to run ok. > > > > > > > _______________________________________________ > 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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Tracula error? set: Variable name must begin with a letter
by Cat Chong 14 Jan '13

14 Jan '13

Hello Experts: I am running the first pre-processing step in Tracula and come across the error: set: Variable name must begin with a letter. Below is an excerpt of the script which seems to be running fine. Did I make a mistake in my dmrirc_single_subject file? Cheers, Catherine fmris-mac-pro-2:8000_tracula fmri$ trac-all -prep -c $SUBJECTS_DIR/dmrirc_single_subject set: Variable name must begin with a letter. INFO: SUBJECTS_DIR is /8000_tracula/ INFO: Diffusion root is /8000_tracula//8000_tracula_out/ Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /8000_tracula//8000_tracula_out//8001_DTI/scripts/dmrirc.local -log /8000_tracula//8000_tracula_out//8001_DTI/scripts/trac-all.log -cmd /8000_tracula//8000_tracula_out//8001_DTI/scripts/trac-all.cmd #------------------------------------- /Applications/freesurfer//bin/trac-preproc #------------------------------------- #@# Image corrections Mon Jan 14 09:37:29 MST 2013 mri_convert /8000_tracula//8001_DTI/IM-0006-0001.dcm /8000_tracula//8000_tracula_out//8001_DTI/dmri/dwi_orig.nii.gz mri_convert /8000_tracula//8001_DTI/IM-0006-0001.dcm /8000_tracula//8000_tracula_out//8001_DTI/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /8000_tracula//8001_DTI/IM-0006-0001.dcm... Starting DICOMRead2() dcmfile = /8000_tracula//8001_DTI/IM-0006-0001.dcm dcmdir = /8000_tracula//8001_DTI Ref Series No = 6 the script continues to run ok.

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mean cluster thickness in qdec
by Berg, S.F. van den 14 Jan '13

14 Jan '13

Dear Freesurfer Experts, I would like the mean thickness measures of each cluster i found in qdec. I used qdec for a group comparison in cortical thickness between a patient group and a healthy control group. I found 5 different significant clusters. I would like to extract the mean cortical thickness of each significant cluster in the patient group and in the healthy control group. If this is not possible the mean cortical thickness of the peak/max vertex is also enough information. Where can i found the file with this information? the problem is what do i have to do? run mri_glmfit-sim? but qdec do not create a .glmdir file? so do i have to run the mri_glmfit first? or is mri_glmfit-sim enough but where is the .glmdir file? I use mri_glmfit-sim --glmdir ?.glmdir --sim mc-z 10000 1.3 mc-z.negative --sim-sign abs --cwpvalthresh 0.5 --overwrite I want to create the csdbase.y.ocn.dat (explaind in mri_glmfit-sim --help) for the mean cluster thickness. This is the file where i can find the mean thickness of each cluster, right? A jpeg file is attached to this email. Many thanks, Stan

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Re: [Freesurfer] Freesurfer fails
by Franklin, Crystal G 14 Jan '13

14 Jan '13

Bruce, I have visually checked the transforms and they do indeed seem incorrect. The images are stretched. I have attached the talairach.xfm for one of the images that failed and one that worked. Thanks for all your help, Crystal On 1/13/13 3:08 PM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: >can you cc the list? Have you visualized the transform to see if it is >indeed incorrect? > >On Sun, 13 Jan 2013, Franklin, Crystal G wrote: > >> I used mri_convert to create the 001.mgz file. In freeview the >>directions appear correct. >> >> Thanks, >> Crystal >> -----Original Message----- >> From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Date: Sun, 13 Jan 2013 09:02:16 >> To: Franklin, Crystal G<FRANKLINC(a)uthscsa.edu> >> Cc: Freesurfer(a)nmr.mgh.harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] Freesurfer fails >> >> Hi Crystal >> >> how did you create the 001.mgz? When you view it in freeview does >> freeview have the correct directions in the anatomy (i.e. I/S, A/P and >> L/R)? >> >> cheers >> Bruce >> On Sat, 12 Jan 2013, Franklin, Crystal G wrote: >> >>> Freesurfer, >>> >>> I have been running a group of subjects through recon-all and some of >>>the >>> subjects are failing at the very beginning of the process and I am not >>>sure >>> why. The images look fine, but I keep getting the following error: >>> >>> #@# Talairach Failure Detection Fri Dec 7 10:54:57 CST 2012 >>> /Applications/freesurfer/subjects/PHY002/mri >>> \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n >>> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm >>> ***FAILED*** (p=0.0013, pval=0.0000 < threshold=0.0050) >>> INFO: Attempting MINC mritotal to perform Talairach align >>> >>> Do you know what could be causing this? >>> >>> I read that you can include the command ?notal ?check to skip this >>>test, but how >>> will this effect my data? If I run this command on the subjects that >>> failed and combine their results with the subjects that worked will my >>>group >>> results be effected? >>> >>> Any help would be appreciated. I have attached one of the log files >>>for a >>> subject that failed. >>> >>> Thanks, >>> Crystal >>> >>> >> >> >> 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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Registering individual subjects to MNI152
by Shantanu Ghosh 14 Jan '13

14 Jan '13

Dear freesurfer experts, I have .sig maps of cortical thickness, curvature and sulcal depth measures from my dataset (two groups: patient, control). I have the following questions: 1) I want to overlay all three maps simultaneously on an average subject created from all subjects' brains, with different color maps. Which command will do this? 2) Register all ?h.thickness datasets to mni152 instead of mni305/fsaveage, convert the files to .mnc/.obj format, and read in Matlab. In this step, do I have to convert the native ras coordinates too? If I want to use bbregister for this step, can you specify the commandline to do this? 3) I want to compute vertexwise expansion/contraction for local surface area, by a) calculating total surface area of all faces connected to a vertex, and then multiplying it with corresponding curv and sulc of that vertex, and b) comparing the result in 3a) with the warpfield from the registration form step 2) above. Or is there something I am missing here? Also, for 3a) how do I get the correct set of triangles for each vertex? Thanks in advance, Shantanu -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging

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Clarification regarding eTIV
by Salil Soman 13 Jan '13

13 Jan '13

Dear List Members, I am planning to use the eTIV for a group analysis using segmentation volumes and I need to confirm that the eTIV ( aka ICV) generated in freesurfer is NOT dependent on the skull strip? Specifically, I wanted to make sure one does not need to QC the skull strips to make sure all of the brain structures suggested in that figure on p728 of the buckner paper ( http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV?action=AttachFile&do=view&tar…) need to be included? Thanks, -S

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What is the correct way to cite Freesurfer in a journal paper?
by john.drozd＠gmail.com 13 Jan '13

13 Jan '13

Hello, I am writing a paper for publication in Neuroimage. I used Freesurfer 4.3 to segment brain anatomy. Lateral ventricles were my focus. Can someone please tell me what is the correct way to cite Freesurfer in a bibliography? Is there a paper I can cite? Thank you, John Drozd John Jan Drozd, M.Sc., Ph.D. Financial Secretary Knights of Columbus St. Pius X Council 10561 Holy Family Parish Post-Doctoral Scholar (Fellow) Imaging Department Robarts Research Institute Western University London, ON, Canada http://publish.uwo.ca/~jdrozd2 http://kong.apmaths.uwo.ca/~jdrozd/personal.html http://kong.apmaths.uwo.ca/~jdrozd/bio.html http://cfmm.robarts.ca/people/staff/bartha-group/#john cell phone: 519-282-3340

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