Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

nii to gii conversion
by Valosek Jan 10 Jul '19

10 Jul '19

External Email - Use Caution Dear Freesurfer experts, I would like to run tractography using probtrackx2 tool from one seed ROI (cortex) through another waypoint ROI. I need both these masks (ROIs) in gii format. Seed ROI I extracted using Freesurfer (recon-all, mri_convert and label2surf functions). Then I drew second waipoint ROI using FSLeyes edit tool, saved it as binary nii.gz file and tried to convert it to surface gii file using mri_vol2surf: mri_vol2surf --src mask.nii.gz --out mask.gii --regheader <SUB> --reg fsl2freesurfer.dat --sd <SUB>/surf --hemi rh --surf pial --projfrac-max 0 1 0.05 --out_type gii But, converted ROI looks empty. Do I have any mistake in command above or is there any another way how to convert nii -> gii? Thanks, Jan

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Re: [Freesurfer] Undefined function or variable called 'fspecial'
by Antonin Skoch 10 Jul '19

10 Jul '19

External Email - Use Caution Hello, Vittal, do you have image processing toolbox of MATLAB installed? The function fspecial is part of this toolbox. Antonin Hello FS experts,I am trying to run the gyrification index and not able to move in the right direction. When execute this command "recon-all -s CSRI005 -localGI" and here is the output copied from the terminal "#@# Local Gyrification Index lh Wed Jul 10 13:15:03 IST 2019 mris_compute_lgi --i lh.pial ================= rm -Rf /usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial ================= rm: cannot remove '/usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz': Permission denied ================= mkdir -p /usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... mghWrite(/usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz, -1): could not open file conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= Academic License >> reading filled volume... closing volume... Undefined function or variable 'fspecial'. Error in make_outer_surface (line 31) Gaussian = fspecial('gaussian',[2 2],1); >> ERROR: make_outer_surface did not create output file '/usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux naren123 4.15.0-54-generic #58~16.04.1-Ubuntu SMP Mon Jun 24 13:21:41 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s CSRI005 exited with ERRORS at Wed Jul 10 13:15:10 IST 2019" Also I have set the MATLAB path for freesurfer and here is the startup.m file "%------------ FreeSurfer -----------------------------% fshome = getenv('FREESURFER_HOME'); fsmatlab = sprintf('%s/matlab',fshome); if (exist(fsmatlab) == 7) addpath(genpath(fsmatlab)); end clear fshome fsmatlab; %-----------------------------------------------------% %------------ FreeSurfer FAST ------------------------% fsfasthome = getenv('FSFAST_HOME'); fsfasttoolbox = sprintf('%s/toolbox',fsfasthome); if (exist(fsfasttoolbox) == 7) path(path,fsfasttoolbox); end clear fsfasthome fsfasttoolbox; %-----------------------------------------------------% " I guess the error is because of 2 different user name: I have matlab license in X name and FreeSurfer can only be executed with root i.e. say Y. I mentioned both the information above. Wanna know the way to sort out this issue asap. Waiting for your reply. Thanks & regards Vittal

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Undefined function or variable called 'fspecial'
by vittal korann 10 Jul '19

10 Jul '19

External Email - Use Caution Hello FS experts, I am trying to run the gyrification index and not able to move in the right direction. When execute this command "recon-all -s CSRI005 -localGI" and here is the output copied from the terminal "#@# Local Gyrification Index lh Wed Jul 10 13:15:03 IST 2019 mris_compute_lgi --i lh.pial ================= rm -Rf /usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial ================= rm: cannot remove '/usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz': Permission denied ================= mkdir -p /usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... mghWrite(/usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz, -1): could not open file conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= Academic License >> reading filled volume... closing volume... Undefined function or variable 'fspecial'. Error in make_outer_surface (line 31) Gaussian = fspecial('gaussian',[2 2],1); >> ERROR: make_outer_surface did not create output file '/usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux naren123 4.15.0-54-generic #58~16.04.1-Ubuntu SMP Mon Jun 24 13:21:41 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s CSRI005 exited with ERRORS at Wed Jul 10 13:15:10 IST 2019" Also I have set the MATLAB path for freesurfer and here is the startup.m file "%------------ FreeSurfer -----------------------------% fshome = getenv('FREESURFER_HOME'); fsmatlab = sprintf('%s/matlab',fshome); if (exist(fsmatlab) == 7) addpath(genpath(fsmatlab)); end clear fshome fsmatlab; %-----------------------------------------------------% %------------ FreeSurfer FAST ------------------------% fsfasthome = getenv('FSFAST_HOME'); fsfasttoolbox = sprintf('%s/toolbox',fsfasthome); if (exist(fsfasttoolbox) == 7) path(path,fsfasttoolbox); end clear fsfasthome fsfasttoolbox; %-----------------------------------------------------% " I guess the error is because of 2 different user name: I have matlab license in X name and FreeSurfer can only be executed with root i.e. say Y. I mentioned both the information above. Wanna know the way to sort out this issue asap. Waiting for your reply. Thanks & regards Vittal

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Postdoctoral Position, University of Oslo
by Dídac Vidal 10 Jul '19

10 Jul '19

External Email - Use Caution I am delighted to advertise the following postdoctoral research fellowship on behalf of Prof Anders M Fjell: At the Center for Lifespan Changes in Brain and Cognition, University of Oslo, Norway, we have an available postdoc position for an excellent candidate with strong skills in functional neuroimaging and linked to the project “The Missing Link of Episodic Memory Decline in Aging: The Role of Inefficient Systems Consolidation”. The position is for a period of 3 years. The researcher will be able to work on uni- and multivariate analyses of high-quality task-related fMRI data acquired at our Siemens Prisma 3T MRI scanner using state-of-the-art sequences (multi-band/multi-echo EPI). Topics currently under investigation in our lab cover cognitive functions during episodic memory operations, as well as mechanisms subserving spatial navigation and spatial working memory. The application deadline is: 18.08.2019 Please see more info here: https://www.jobbnorge.no/en/available-jobs/job/172827/postdoctoral-research… P.S. Interested candidates are welcome to contact Anders M Fjell a.m.fjell(a)psykologi.uio.no All the best, Dídac -- Dídac Vidal Piñeiro

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mris_make_surfaces -aseg filled vs -noaseg (difference v5.3 and v6)
by Scott Love 09 Jul '19

09 Jul '19

External Email - Use Caution Hello all, To create surfaces for a sheep brain using Freesurfer version 5.3 I previously used, mris_make_surfaces -mgz -noaparc -aseg filled -T1 brain.finalsurfs $subj rh, and it worked great. Running the same command using version 6 (freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c) I get this error: “… generating cortex label... 1 non-cortical segments detected only using segment with 71880 vertices LabelErode: NULL label No such file or directory LabelDilate: NULL label No such file or directory Segmentation fault: 11” When changing the command to ( mris_make_surfaces -mgz -noaparc -noaseg -T1 brain.finalsurfs $subj rh ) it runs without error. However, the result is clearly not as good - the pial surface looks like a slightly extended/inflated white surface. This is also true for a brain that worked perfectly with version 5.3. From the error I am guessing that labels in filled (127 and 255) are not those required. Is it (still) possible to use filled.mgz as the input to -aseg in mris_make_surfaces? Is it perhaps possible to modify the label numbers in filled.mgz to get this working again? Thanks, Scott

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Desikan atlas
by Pinar Pnr 09 Jul '19

09 Jul '19

External Email - Use Caution Hi dear Freesurfer users, Is there a version of Desikan atlas in MNI space? Bset Regards, Pinar

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pial.lgi
by vittal korann 09 Jul '19

09 Jul '19

External Email - Use Caution Hi FS experts, I wanted to run the gyrification index for all patients with Schizophrenia and volunteers. When I entered the command: "recon-all -s SATM124 -qcache -measure pial_lgi" and the terminal output " Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 root 1590 1054464 Jul 6 16:02 /usr/local/freesurfer/subjects/SATM124/scripts/recon-all.log Linux naren123 4.15.0-52-generic #56~16.04.1-Ubuntu SMP Thu Jun 6 12:03:31 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux '/usr/local/freesurfer/bin/recon-all' -> '/usr/local/freesurfer/subjects/SATM124/scripts/recon-all.local-copy' #-------------------------------------------- #@# Qdec Cache preproc lh pial_lgi fsaverage Sat Jul 6 16:39:03 IST 2019 /usr/local/freesurfer/subjects/SATM124/surf mris_preproc --s SATM124 --hemi lh --meas pial_lgi --target fsaverage --out lh.pial_lgi.fsaverage.mgh nsubjects = 1 ERROR: cannot find /usr/local/freesurfer/subjects/SATM124/surf/lh.pial_lgi Linux naren123 4.15.0-52-generic #56~16.04.1-Ubuntu SMP Thu Jun 6 12:03:31 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s SATM124 exited with ERRORS at Sat Jul 6 16:39:03 IST 2019 For more details, see the log file /usr/local/freesurfer/subjects/SATM124/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting" There is no file called 'lh.pial_lgi" in the surf directory for all subjects. I'm using freesurfer version6.0. Would appreciate any help. Thanks & regards -Korann Thanks & regards Vittal

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Re: [Freesurfer] Doubts in hippocampal subfields labeling
by Antonin Skoch 08 Jul '19

08 Jul '19

External Email - Use Caution Dear Eugenio, I have uploaded the subject as file hippocampal_subfields_labeling.tar.gz to your server surfer.nmr.mgh.harvard.edu. RAS coordinates of the unlabeled area are -31,-27,-9. Thank you in advance, Antonin Dear Antonin, It is difficult to see what’s going on in the images you sent. Would you mind uploading the subject, or at least sending us the image without the segmentation overlaid (and ideally, a sagittal view as well)? Cheers, /Eugenio-- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-boun...(a)nmr.mgh.harvard.edu> on behalf of Antonin Skoch <a...(a)ikem.cz> Reply-To: Antonin Skoch <a...(a)ikem.cz>, Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, 2 July 2019 at 21:43 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Doubts in hippocampal subfields labeling External Email - Use Caution Dear experts, I noticed that systematically in most of my subjects there is area in hippocampal region, labeled in aseg as hippocampus, but NOT labeled as hippocampus in hippocampal subfields segmentation (it has zero value there). See screenshots with norm.mgz overlaid by 1) aseg, 2) hippocampal subfields segmentation. According to T1 and T2 signal, it should neither be white matter and also probably not a ventricle/CSF. Neocortex is not located here. It has similar signal intensity as hippocampus, so I think that it should be hippocampus, but I am puzzled by hippocampal subfields segmentation results there. Why it is not labeled? Could you please help me to clarify this? My concern is to correctly label this area. I could upload the example subject if it is of any help. Regards, Antonin Skoch

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Re: [Freesurfer] Freesurfer Digest, Vol 185, Issue 11
by Mahshid Fouladivanda 08 Jul '19

08 Jul '19

External Email - Use Caution Dear Bruce, All the outputs are .nii and .gii I do not know if it is possible to convert it to the annotation! By the way, what is needed for creation of the annotation file? I mean what information, it needs? Regards Mahshid From: freesurfer-request(a)nmr.mgh.harvard.edu To: freesurfer(a)nmr.mgh.harvard.edu Date: Mon, 08 Jul 2019 11:34:24 -0400 Subject: Freesurfer Digest, Vol 185, Issue 11 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: Skull Strip (Bruce Fischl) 2. How to Divide the Surface Parcellations of the Brain (Mahshid Fouladivanda) 3. Re: How to Divide the Surface Parcellations of the Brain (Bruce Fischl) 4. Assigning voxels different intensity values (Fotiadis, Panagiotis) 5. Re: Assigning voxels different intensity values (Bruce Fischl) 6. Re: Assigning voxels different intensity values (Fotiadis, Panagiotis) 7. Re: Assigning voxels different intensity values (Bruce Fischl) 8. Re: Assigning voxels different intensity values (Fotiadis, Panagiotis) 9. how to map regional t values on surface (fengmei fan) 10. Skull Strip (Admin) 11. Error in analyze (Qdec) (Abby tang) 12. Re: Freesurfer Digest, Vol 185, Issue 9 (vittal korann) 13. Postdoctoral Position opening at the University of Pittsburgh in neuroimaging of mood disorders (Anna Manelis) 14. Re: make_average_subject error: could not load norm volume from (null) (Greve, Douglas N.,Ph.D.) 15. Re: Skull Strip (Hoopes, Andrew) 16. Re: recon-all error: Correcting defect (Diamond, Bram Ryder) 17. Re: recon-all error: Correcting defect (Miguel ?ngel Rivas Fern?ndez) ---------------------------------------------------------------------- Message: 1 Date: Sun, 7 Jul 2019 13:33:35 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Skull Strip To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1907071333050.916(a)door.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" I believe I already answered this. I don't understand what amplified noise you mean. The brainmask.mgz can be used with mri_mask to apply to any input volume you want. cheers Bruce On Sun, 7 Jul 2019, Admin wrote: > > ????????External Email - Use Caution???????? > > Dear Freesurfer group? Now,I want ?generated a brain mask including the brain but excluding the > amplified noise regions after skull strip, but I can't find the corresponding command line, so I > send this email to you,?hoping to get your help.? > My English is poor, if?I make mistakes ,?I hope you can understand me. Thanks for your help? > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Sincerely: Meng Nan Lin > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Date: 07/04/2019 > > > > > ? > > > > > ? > > > ------------------------------ Message: 2 Date: Mon, 08 Jul 2019 01:06:44 +0430 From: "Mahshid Fouladivanda" <M.Fouladivanda(a)sutech.ac.ir> Subject: [Freesurfer] How to Divide the Surface Parcellations of the Brain To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <WC20190707203644.661057(a)sutech.ac.ir> Content-Type: text/plain; charset="us-ascii" External Email - Use Caution Dear Freesurfer Experts, I would like to divide the surface parcellations of the neonatal brain. The parcells were extracted using Draw_EM (Developing brain Region Annotation With Expectation-Maximization), an atlas based segmentation, from cortical and sub-cortical. As I understand from help comments, mris_divide_parcellation would help, but it needs annotation file to be imported as input. I do not have the annotation file. I would appreciate it if you could help me how to divide my parcells in more regions? Regards, Mahshid

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recon-all error: Correcting defect
by Miguel Ángel Rivas Fernández 08 Jul '19

08 Jul '19

External Email - Use Caution I ran the recon-all in one subject and and this process was stopped in the topology correction. In particular during the "CORRECTING DEFECT 36 (vertices=19847, convex hull=5892, v0=94733)". I reviewed the lh.inflated.nofix and the lh.orig.nofix files in Freeview and I noticed that the this error would be located in the lh.inflated.nofix file. I am not completely sure but I suspect that this error may be due to the fact that there is a large amount of brain lesion and this would difficult the topology correction. How can I fix this problem? Thanks in advance. Best regards, -- *Miguel Ángel Rivas Fernández*

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