Freesurfer March 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
229 discussions

Postdoc job: Neuroimaging of mood disorders in adolescence at University of Cambridge
by Kirstie Whitaker 16 Mar '16

16 Mar '16

Dear FSL, Freesurfer and Neuroimaging in Python list members (with apologies for cross posting), The closing date for this position is this SUNDAY 20th MARCH, so you don't have much time (although we only need a cover letter and CV type details for your application), but I've been asked to reach out to you because we'd really like to hire the very best postdoc for this role at the University of Cambridge. Please share this email widely with your personal and professional networks. The successful applicant will join a multidisciplinary team of scientists investigating the neural basis and cognitive correlates of behavioural phenotypes in large existing and still being collected longitudinal community and clinical cohorts of adolescents and young adults as part of the Neuroscience in Psychiatry Network (http://nspn.org.uk) Applicants will have a PhD and some postdoctoral experience reflecting an expert level of knowledge in cognitive and behavioural neuroscience together with a working knowledge and interest in longitudinal data analysis and mental illness. The full job advert and instructions on how to apply are at http://www.jobs.cam.ac.uk/job/9696. The role comes with an invitation to interview for a fellowship at Peterhouse, the oldest remaining college in Cambridge. The start date is (reasonably) flexible but projected for May 2016. The funds for this post are available until 31 March 2018 in the first instance. The Clinical School at the University of Cambridge is a proud holder of an Athena SWAN Silver award <http://athena-swan.medschl.cam.ac.uk/> and candidates from groups that are under-represented in senior STEMM positions (such as women and people of colour) are particularly encouraged to apply. If you have any informal questions about this vacancy please contact Professor Ian Goodyer (ig104(a)cam.ac.uk) For information on the application process for this vacancy, please contact Dominic Drane, HR Administrator via email on hradminpsychiatry(a)medschl.cam.ac.uk. Please quote reference RN08523 on your application and in any correspondence about this vacancy. Thank you Kirstie Whitaker -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge *Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB *Phone: *+44 7583 535 307 *Website:* www.kirstiewhitaker.com

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Re: [Freesurfer] Editing Lesions in FreeSurfer 5.1
by Allison Rainford 15 Mar '16

15 Mar '16

Hi Bruce, I?ve attached a screen shot of a temporal pole of one of the brains that we have had issues with. Here the issue is that there is a lesion without a very clear boundary for the white matter and freesurfer was unresponsive to simply using white matter edits (placing 255s on the wm.mgz), and so we tried placing control points where we think the white matter boundary should lie. However, we know that control points should not be placed in these dark spots of a lesion. Thank you, Allison

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Recon Reprocessing Issues
by Champe Barton 15 Mar '16

15 Mar '16

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Cortical thickness analysis -- Qdec
by Alshikho, Mohamad J. 15 Mar '16

15 Mar '16

Hi Doug, I have two groups of subjects and I want to study the difference in cortical thickness between the groups. I used Qdec to run the analysis and I got significant difference between the groups in areas support what I am looking for. I repeated the analysis as mentioned in Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis 1. My data is previously cached so I ran the command : mris_preproc --fsgd gender_age.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.gender_age.thickness.10.mgh 2. GLM analysis: mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd gender_age.fsgd dods --C lh-Avg-thickness-age-Cor.mtx --surf fsaverage lh --cortex --glmdir lh.gender_age.glmdir 3. Correction for multiple comparison mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 4 neg --cwp 0.05 --2spaces Surprisingly, the results are totally different from what I get in Qdec. I checked Qdec's commands generated in Terminal and I noticed that it uses the command "mri_surfcluster" instead of " mri_glmfit-sim " Kindly, 1. What is the difference between "mri_surfcluster" and " mri_glmfit-sim " 2. Is it expected that we get different results as an output of the previous two different methods 3. In order to run statistical analysis regarding volumetrics and cortical thickness. Which method is more advisable, Qdec or the previous command lines (1-3) Best, Mohamad

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Upgrading to OS X EL Capitan
by Elissa Ash 15 Mar '16

15 Mar '16

Dear Freesurfer experts, I have been working with freesurfer V5.3 on the Mac OS 10.8.5. My institution is requesting that I upgrade the OS on my computer to OS X El Capitan (10.11). Will this change my ability to look at or process freesurfer data? Will the recons that I have done be compatible? If I do more recons then can I still compare the data to those done on OS X 10.8.5? Is it recommended that I upgrade to OS or should I not do it? Thank you kindly for your help, Elissa -- Elissa Ash, MD, PhD Director, Center for Memory and Attention Disorders Department of Neurology Tel Aviv Sourasky Medical Center 6 Weizmann St. Tel Aviv 64239, Israel 972-3-6973698 fax: 972-3-695-0365

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voxel vs surface based morphometric analysis
by John Anderson 15 Mar '16

15 Mar '16

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Re: [Freesurfer] 3_group_comparison
by Lee Tirrell 15 Mar '16

15 Mar '16

Hi Dusan, setenv is used when you are using tcsh. since you are using bash, you can run this command to set your language: export LANG=en_US.UTF-8 Hope this helps. Best, Lee On Tue, 29 Sep 2015, Dusan Hirjak wrote: > Thank you very much for your suggestion. Now it has worked well. > However, I am having trouble running the simulation via: > > mri_glmfit-sim --glmdir NSS_3_GR.glmdir --cache 4 abs --cwp 0.05 --2spaces > > ERROR: thresh = 4,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 > > > Where can I set up the EN language with "setenv LANG en_US.UTF-8"? > > > I am getting this message: > > > bash-3.2$ setenv LANG en_US.UTF-8 > > bash: setenv: command not found > > > How can I change the language? > > > Many thanks! > > Dusan > > ___________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ > From: rpwang(a)nmr.mgh.harvard.edu > Date: Mon, 28 Sep 2015 19:35:12 -0400 > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] 3_group_comparison > > Was the path of the overlay file correct? It looks like it can’t find the file. Try providing the full path of the overlay file in the freeview command. > > Best, > Ruopeng > > On Sep 28, 2015, at 6:46 PM, Dusan Hirjak <dusanhirjak(a)hotmail.com> wrote: > > Many thanks!!!, yes, freeview has opened, but I am still not seeing any results, just the "lh.inflated" > It says: "Failed to load surface overlay" > > and than I got the following message: > > bash-3.2$ freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d > 2015-09-29 00:41:53.887 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.889 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.905 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.906 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.921 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.922 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.939 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.939 Freeview[22049:303] invalid drawable > Did not find any volume geometry information in the surface > ø;C 8Íÿ¿ø;C È+’Àá > > 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) > mghRead(/users/dhirjak/MRI/Freesurfer_2/NSS_LGI/fsaverage/surf/lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh, -1): could not open file > mghRead(/users/dhirjak/MRI/Freesurfer_2/NSS_LGI/fsaverage/surf/lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh, -1): could not open file > could not read overlay data from /users/dhirjak/MRI/Freesurfer_2/NSS_LGI/fsaverage/surf/lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh > mghRead(/users/dhirjak/MRI/Freesurfer_2/NSS_LGI/fsaverage/surf/lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh, -1): could not open file > 2015-09-29 00:42:02.445 Freeview[22049:303] modalSession has been exited prematurely - check for a reentrant call to endModalSession: > > I dont understand the problem. Do you have any ideas??? > > Thank you! > > Dusan > > > > > To: freesurfer(a)nmr.mgh.harvard.edu > > From: greve(a)nmr.mgh.harvard.edu > > Date: Mon, 28 Sep 2015 18:33:50 -0400 > > Subject: Re: [Freesurfer] 3_group_comparison > > > > I think it needs a -f before the surface > > > > On 09/28/2015 06:27 PM, Dusan Hirjak wrote: > > > Many thanks, yes, it did work well. > > > > > > But, than I ran "freeview > > > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.NSS_3_GR.glmdir/AvG-thickness-NSS-Cor/sig.mgh:overlay_threshold=4,5 > > > -viewport 3d" > > > > > > and got the following message: > > > > > > bash-3.2$ freeview > > > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.NSS_3_GR.glmdir/AvG-thickness-NSS-Cor/sig.mgh:overlay_threshold=4,5 > > > -viewport 3d > > > > > > 2015-09-29 00:23:47.366 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.367 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.385 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.386 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.399 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.400 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.420 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.421 Freeview[22019:303] invalid drawable > > > > > > Unrecognized sub-option flag 'annot=aparc.annot'. > > > > > > > > > Freeview has opened, but it showed no results at all:-( > > > > > > > > > What should I do? I read that one has to upgrade the newest > > > freeview-version? Is it possible to get the newest version without > > > installing freesurfer again? > > > > > > Many thanks! > > > > > > Dusan > > > > > > > > > ------------------------------------------------------------------------ > > > Date: Mon, 28 Sep 2015 11:35:50 -0400 > > > From: greve(a)nmr.mgh.harvard.edu > > > To: freesurfer(a)nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] 3_group_comparison > > > > > > Did you include the back slashes in your command? If so, remove them > > > and retry. > > > > > > On 9/25/15 7:11 PM, Dusan Hirjak wrote: > > > > > > Dear Freesurfer experts, > > > > > > I am trying to compare 3 groups (aut, sch, ges) according to > > > thickness, area and LGI at once (omnibus test). > > > > > > I did run the following command: > > > > > > mris_preproc --fsgd NSS_3_GR.fsgd \ --cache-in > > > thickness.fwhm15.fsaverage \ --target fsaverage --hemi lh \ --out > > > lh.NSS_3_GR.thickness.15.mgh > > > > > > > > > This step did work properly:-) > > > > > > > > > > > > Now, Im trying to run the following command, but it does not work: > > > > > > > > > mri_glmfit \ --y lh.NSS_3_GR.thickness.15.mgh \ --fsgd > > > NSS_3_GR.fsgd dods\ --C contrasts.mtx \ --surf fsaverage lh \ > > > --cortex \ --glmdir NSS_3_GR.glmdir > > > > > > > > > I got this message: "ERROR: Option--y unknown" > > > > > > > > > What am I doing wrong? > > > > > > > > > Thank you for your help! > > > > > > > > > > > > Best regards > > > > > > > > > Dusan > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > _______________________________________________ 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. > > > > > > > > > _______________________________________________ > > > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ 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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Volumes of individual subject based on 001.mgz or nu.mgz?
by Kaiming Yin 15 Mar '16

15 Mar '16

Dear guys, Could I ask in the process of each individual data, are the volumes in the aseg.stat file or other files in the stats/ folder based on the 001.mgz data or the nu.mgz data, or others? It seems there is a bit transformation from the 001.mgz to the nu.mgz, is this true? And will this transformation affect the volumes then? Thanks, Kaiming

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mri_glmfit-sim
by John Anderson 15 Mar '16

15 Mar '16

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mri_binarize
by Alshikho, Mohamad J. 15 Mar '16

15 Mar '16

Hi Doug, I would like to inquire about the command " mri_binarize". In the past, this command was able to create a binarized nifti mask from aseg.mgz, wmparc.mgz .... etc without the need to convert the output "mgz" files to nifti. In other words If I want to create a mask for the precentral gyrus I was using the following: mri_binarize --i aseg.mgz --o precentral.nii --match 1024 The command was able to create the mask and convert it to nifti file at once, but right now if the output is nifti file, it returns empty so I need to make the output "mgz" then convert it to nifti!! Is this real or I am missing something? Thanks for any advice! By the way I see this issue came up recently and in both freesurfer V 5.3 and V6 Best, Mohamad

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Freesurfer March 2016