Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

Freesurfer on new Mac (apple silicon-chip)
by Correia de Aguiar, V.M. 04 Dec '20

04 Dec '20

External Email - Use Caution Hi, I am about to buy a new laptop and I am wondering if freesurfer will be running on the new mac? I mean, Mac OS big sur (with apple silicon chip, where they no longer use an intel processor). Many thanks for your advice. Best, Vânia de Aguiar, PhD Assistant Professor in Neurolinguistics University of Groningen Faculty of Arts Oude Kijk in 't Jatstraat 26 Room 1315.0408 9712 EK, Groningen The Netherlands

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Fwd: Longitudinal pipeline
by vittal korann 04 Dec '20

04 Dec '20

External Email - Use Caution Hello FS experts Thank you for your kind response. This is regarding my previous mail. I think we need to talk about the design matrix X first (sorry, I did not look at your xlsx file; I think it's probably better to send simple csv files if at all). I attached longitudinal data in csv format. Besides the covariates that you mention, the matrix needs to contain an intercept, a variable for ?time?, a variable for ?group? (assuming you have a control group also), and a group-by-time interaction term in order to asses differential change over time (again, if you have a control group). I do not have a control group. Right now I have only schizophrenia patients who underwent 2 scans: the first is the baseline and the second one is after 3 months of yoga therapy. Wish to know how can I proceed with my available data. Just to make sure: ?age? should be ?age at baseline? (i.e. constant across time per subject), otherwise, it will be confounded with time. Yes, I used the same across the study. Could you review (and possibly adapt) your design matrix X with respect to which columns it contains, and write it in the reply? I tried but couldn't get there. Looking forward to your response. Thanks, Vittal

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recon-all issues debugging
by Courtney Haswell 03 Dec '20

03 Dec '20

External Email - Use Caution I am trying to debug why all of our T1's are failing Freesurfer recon-all. It seems that most of the files are being created but it isn't getting to the stats steps to output those files. In the recon-all log it does say "recon-all -s 13265 exited with ERRORS." I looked in the recon-all.error file and the only thing in that is "CMD mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix." Would this be the step where the error is happening? I have checked the T1 thoroughly and it is good quality. What is the best way to debug why this is happening with our scans?

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segmentHA_T1.sh
by Erik Lindberg 03 Dec '20

03 Dec '20

External Email - Use Caution Hi, I am trying to run the segmentHA_T1.sh with the suffix CA but I seem not be able to write the call correctly How should I call this? best Olof

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Re: [Freesurfer] tkregister issue with reg-feat2anat {Disarmed}
by Walsh, Erin 02 Dec '20

02 Dec '20

External Email - Use Caution Hi Dr. Greve, Our IT team replaced the reg-feat2ant file on the university HPC. When I reran a test subject, it resulted in a "command not found" error. See attached screenshot. I notified IT and they stated the following: "Since the only change made by admins was putting that new file in place, so they just put the old file back in place. You can try running the script again to see if that 'command not found' error goes away. If not, then you need to report the error back to the author that provided the file. " With the previous reg-feat2anat file, the bug I initially emailed about replicated. Do you have any suggestions for what may be causing the error? Thanks! Erin https://secure-web.cisco.com/1Xt5TzuhfYGMFSQ1E2hCKW008efsUaiJNMtBUxoHORy7dS… -- Erin Walsh, Ph.D. Assistant Professor University of North Carolina-Chapel Hill Department of Psychiatry Chapel Hill, NC 27599-3367 erin_walsh(a)med.unc.edu pronouns: she/her ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Thursday, November 12, 2020 12:00 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Freesurfer Digest, Vol 201, Issue 19 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://secure-web.cisco.com/1PrXXNA2YRR-YEzLxXK-oIH4gfUWRVVoD9R3JNaZFZF8kG… 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: Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} (???) 2. Re: tkregister issue with reg-feat2anat {Disarmed} (Douglas N. Greve) 3. Re: Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} (Douglas N. Greve) 4. Re: Sulc maps (Douglas N. Greve) 5. Re: Help with MRI labels (Douglas N. Greve) 6. mris_pmake error - freadFloat: fread failed (Nasr, Shahin,Ph.D.) 7. Support: Password Request for Ubuntu_710 to download Freesurfer on Windows 10 {Disarmed} (Park, James) 8. Re: Support: Password Request for Ubuntu_710 to download Freesurfer on Windows 10 {Disarmed} {Disarmed} (fsbuild) 9. Re: Help with MRI labels {Disarmed} (Alberto Del Cerro Leon) ---------------------------------------------------------------------- Message: 1 Date: Thu, 12 Nov 2020 18:39:44 +0800 (GMT+08:00) From: ??? <mengjun(a)csu.edu.cn> Subject: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} To: "Freesurfer support list" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <6071ada5.3fd7.175bc0a2c24.Coremail.mengjun(a)csu.edu.cn> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Thank you very much, I get lh_areapial.avgwf.dat and lh_areapial.sum file after the mri_segstats command (1) Does the lh_areapial.avgwf.dat contain areas value for all my subject? (2) When I extract the volumes, the lh_volume.sum displays the unit for the volume is Area_mm2?Blue color). Is this correct? ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 161058 81037.1 Seg0000 242940.3281 0.7312 0.0000 3.8885 3.8885 2 1 2784 1182.3 Seg0001 3760.6619 0.2525 0.7136 1.8140 1.1005 Following is the code for extracting volumes mri_segstats --i qdec/Volume_15_L/y.mgh (y.mgh was created after Qdec) --slabel fsaverage lh lh.volume.label (This was the label extracted from the fsaverage after multi-correction) --avgwf lh_volume.avgwf.dat (output file) --accumulate --sum lh_volume.sum (output file) -----????----- ???:"Douglas N. Greve" <dgreve(a)MGH.HARVARD.EDU> ????:2020-11-11 23:58:20 (???) ???: freesurfer(a)nmr.mgh.harvard.edu ??: ??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} Sorry, try this mri_segstats --i qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec) --slabel fsaverage lh lh.areapial.label (This was the label extracted from the fsaverage after multi-correction) --avgwf lh_areapial.avgwf.dat (output file) --accumulate --sum lh_areapial.sum (output file) On 11/5/2020 10:26 PM, ??? wrote: External Email - Use Caution I tried following codes according to the suggestions, the terminal reported an error: cannot do frame average without input volume mri_segstats --seg qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec) --slabel fsaverage lh lh.areapial.label (This was the label extracted from the fsaverage after multi-correction) --avgwf lh_areapial.avgwf.dat (output file) --accumulate --sum lh_areapial.sum (output file) -----????----- ???:"Douglas N. Greve" <dgreve(a)MGH.HARVARD.EDU> ????:2020-11-05 22:37:07 (???) ???:freesurfer@nmr.mgh.harvard.edu ??: ??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} Try --slabel fsaverage lh /path/to/lh.areapial.label On 11/2/2020 10:24 PM, ??? wrote: External Email - Use Caution Thank you very much! I tried to extract the areas with the following codes: mri_segstats --seg qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec) --slabel lh.areapial.label (This was the label extracted from the fsaverage after multi-correction) --avgwf lh_areapial.avgwf.dat (output file) --accumulate --sum lh_areapial.sum (output file) I did not get a text file including the areas of all subjects. Is this code correct? -----????----- ???:"Douglas N. Greve" <dgreve(a)mgh.harvard.edu> ????:2020-11-02 23:36:14 (???) ???:freesurfer@nmr.mgh.harvard.edu ??: ??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} I think the reason for this may be that the data in fsaverage space (after mris_preproc) will have had a jacobian correction which will not be in data on the native surface. For this reason, I would not use #1. #2 is fine.You can apply your label in fsaverage space to the y.mgh used as input to mri_segstats specifying the label using --slabel and using --avgwf output and also use --accumulate; run it with --help for more info. This will create a text file of the areas or volumes (depending upon which y.mgh you input) all your subjects for that label. On 10/30/2020 10:37 PM, ??? wrote: External Email - Use Caution Dear Professors: I compared the thickness, area, volume in the mild traumatic brain injury patients with health control by FreeSurFer, and found statistic difference region in the cortex area, volume respectively. I defined the statistic difference regions as a label on the fsaverage and mapped this label to subjects by Qdec/mri_label2label. The label defined on the fsaverage was mapped onto all subjects successfully, and the label in subjects matched well with the inflated cortex of subjects in Freeview Then the value of the label in every single subjects was extracted, and I found that there is no statistic difference in the value regarding to the area and volume between the mild traumatic brain injury patients and health control subjects. Following are my questions: (1)Can I carry out correlation analysis between the cortex area and volume with the behavior scores through these non-statistical extracted values? (2)Can I extract the value of cortex area and volume in the standard space for every TBI and health control subjects, and carry out correlation analysis between the cortex area and volume with the behavior scores. How can I extract the value of cortex area and volume in the standard space for every TBI and health control subjects Best wishes Mengjun Li -----????----- ???:"Douglas N. Greve" <dgreve(a)MGH.HARVARD.EDU> ????:2020-10-30 23:40:30 (???) ???:freesurfer@nmr.mgh.harvard.edu ??: ??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject Do you mean you compared your TBI subjects against fsaverage? That is not proper methodology. On 10/29/2020 9:51 PM, ??? wrote: External Email - Use Caution Dear FreeSurfer Developers: I compared the cortical thickness, area, volume in the mild traumatic brain injury patients with health control by FreeSurFer, and found a statistic difference region in the cortex area and volume after correction. How can I extract the value of cortex area and volume for every subject in the fsaverage with the code of mri_segstats FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: macOS High Sierra. Best wishes Mengjun Li Second Xiangya Hospital Central South University _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1XuArL9u2F6UeXtxWprizR8bwWe0Fw6TQOEze4B98CIjQd… _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1XuArL9u2F6UeXtxWprizR8bwWe0Fw6TQOEze4B98CIjQd… _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1XuArL9u2F6UeXtxWprizR8bwWe0Fw6TQOEze4B98CIjQd… _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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extracting mask for basal ganglia, deep grey, and centrum semiovale
by miracle ozzoude 02 Dec '20

02 Dec '20

External Email - Use Caution Hello Experts, I did like to create a mask for basal ganglia, deep grey matter, and centrum semiovale. I know how to extract the mask for the first 2 (using aseg.mgz) however, how do I extract the last one. What mask should I use to extract the centrum semiovale? I don't want to include the cerebellar white matter. Thanks. Best, Paul

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Aligning functional and structural scans with FsFast
by Karan Desai 02 Dec '20

02 Dec '20

External Email - Use Caution Hi FreeSurfer developers, I have Freesurfer anatomical data from recon-all, and pre-processed functional data in NifTI format from FSL and you would like to use FsFast to align that data. What would be the best way to do that using FsFast? Is this possible? Thanks.

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mri_surf2surf lh.area does not match surface (148208, 146833)
by 1248742467 02 Dec '20

02 Dec '20

External Email - Use Caution Hello, Fs When I run the following command: mri_surf2surf --srcsubject HLN-12-2 --sval area --src_type curv --trgsubject fsaverage5 --trgsurfval /home/tj/application/freesurfer/subjects/min_template/HLN-12-2-target/area --trg_type curv --hemi lh the error message: Reading curvature file /home/tj/application/freesurfer/subjects/HLN-12-2/surf/lh.area ERROR: number of vertices in /home/tj/application/freesurfer/subjects/HLN-12-2/surf/lh.area does not match surface (148208,146833) Not only the area, volume and jac.white have the same problems. Do you know how to solve it? Looking forward to your reply.

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Issue with custom label
by Catherine Tallman 02 Dec '20

02 Dec '20

External Email - Use Caution Hello, After running mri_vol2label I created a custom label named test.label. When I try to load the label onto lh.pial, I receive the following error: "Could not load label from <path>". The file is saved within the path folder itself. Within the terminal I receive the warning "label has not been mapped to surface". I was wondering what might be causing this issue? Attached is the label file. mri_vol2label --c mri/aparc+aseg.mgz --id 1016 --l label/lh.parahippocampal. label Thank you, Catherine -- ------------------------------------------------ Catherine Tallman, M.A. Graduate Student CNS Laboratory of Memory and Brain University of California, San Diego

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About mri_vol2surf
by Alberto Del Cerro Leon 02 Dec '20

02 Dec '20

External Email - Use Caution Hello everyone, I tried to follow your instruction about how to get the fresurfer stats in AAL ROIs. I have an image .nii with the labels of the AAL in the MNI space (i submit this image in the e-mail). Can I use this image in the mri_vol2surf? If so, i suppose that this image would be the input one, but i don't know what is registration file in the syntax of mri_vol2surf Sorry for the inconvenience, Alberto

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