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30086 discussions

Negative Longitudinal Hippocampal Subfield Values
by Ashwati Vipin (NNI) 13 Jul '20

13 Jul '20

External Email - Use Caution Dear FreeSurfer Developers, I think my earlier email may have gotten lost. I've run the longitudinal hippocampal subfield pipeline using the following command on freesurfer version 6.0: longHippoSubfieldsT1.sh PAWS001_base_FS I received no errors and everything seems to have run fine. But on computing the subfields using the following command: quantifyHippocampalSubfields.sh T1.long PAWS_longitudinalhipsubfields.txt I noticed that all of subfields have negative volume values. I checked the individual text files within each subject's timepoint and indeed the output is showing negative volumes. I have also tested the same subject and run the cross-sectional hippocampal subfield pipeline using the following command: recon-all -s PAWS001_TP1_FS -hippocampal-subfields-T1 I'm really not sure why the longitudinal pipeline is showing negative values. Could it be a Freesurfer version issue? Am I doing something wrong? It is especially mind-boggling since I receive no error and the command is running smoothly! Please help. I have attached the text files of the same subject run cross-sectionally and longitudinally. 1. A single subject processed cross sectionally - lh.hippoSfVolumes-T1.v10.txt 2. The same subject process longitudinally - lh.hippoSfVolumes-T1.long.v10.txt Thank you so much!! Best regards, Ashwati [cid:image9b8575.PNG@bec4f33e.43bdc947] nnitagl1

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Re: [Freesurfer] discontiguous regions assigned to same label by mris_divide_parcellation
by Mcnorgan, Christopher 11 Jul '20

11 Jul '20

External Email - Use Caution Thanks Bruce, The effect can be replicated on the attached .annot in fsaverage space. Step 1: MacBook-Pro:label chris$ mris_divide_parcellation fsaverage lh ABCD_task_p001.annot 1600 ABCD1600 Step 2: MacBook-Pro:label chris$ mris_divide_parcellation fsaverage lh ABCD1600.annot 400 ABCD400 You should find that the large ventral temporal cluster in lh.ABCD400.annot has three of pairs of discontiguous clusters with the same label name. Thanks for your help!

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discontiguous regions assigned to same label by mris_divide_parcellation
by Mcnorgan, Christopher 11 Jul '20

11 Jul '20

External Email - Use Caution I’ve been using the .annot files generated by group-level GLM results for functional masks for task-related functional connectivity studies. Depending on threshold and contrast, the clusters can be quite large, and I would prefer to use the mris_divide_parcellation utility to break the clusters up into smaller subregions, and generally use the size threshold to make the regions roughly equal size. One quirk of mris_divide_parcellation is that, because it divides along the longest axis, if I want my final region sizes to be small (relative to the size of the whole cluster), I often find that the subdivisions take on the form of many narrow bands perpendicular to the axis of division. I have attempted to combat this by applying the utility in two passes: in the first pass, I might call: mris_divide_parcellation fsaverage lh mycontrast.annot 1600 mycontrast_1600 This first breaks up large clusters into 1600mm2 subclusters along their longest axes If my goal is to have 400mm regions, I then call mris_divide_parcellation on the new annotation: mris_divide_parcellation fsaverage lh mycontrast_1600.annot 400 mycontrast_400 This has the desired effect of generating roughly 400mm regions that are roughly square, at least, compared to the very narrow regions I would have gotten had I just done a single pass using 400mm subdivisions from the original annotation. The problem I am having is that the subdivisions in the second pass appear to be assigning discontiguous subdivisions of the same source cluster to the same label. An example is attached. The subdivisions have the proportions I’m looking for, but two regions at opposite ends of the same cluster have the same label (there are actually three pairs of noncontiguous regions with the same label in this large cluster). I am wondering if there is any way that this can be avoided? [cid:373867F5-ADB4-4D59-86B1-8384131E3822] /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/

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Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
by Iglesias Gonzalez, Juan E. 10 Jul '20

10 Jul '20

Sorry! function Icropped=applyCropping(I,cropping) i1=cropping(1); j1=cropping(2); k1=cropping(3); i2=cropping(4); j2=cropping(5); k2=cropping(6); Icropped=I(i1:i2,j1:j2,k1:k2,:,:,:,:,:,:,:,:,:,:); Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Jenna Katherine Blujus <jkblujus(a)uwm.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, July 10, 2020 at 18:32 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment External Email - Use Caution Hi Eugenio, Ok, great! The inpaint script requires the applyCropping function. I tried finding a copy of the function on github but was unsuccessful. Do you have a copy of the applyCropping function? Thanks, Jenna ________________________________ From: Jenna Katherine Blujus <jkblujus(a)uwm.edu> Sent: Thursday, July 9, 2020 8:05 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: Freesurfer Hippocampal Subfield Misalignment Hi Eugenio, Sorry! Can you specify how to copy the edits from aseg to wmparc within Matlab? aseg=MRIread('aseg.presurf.mgz') wmparc=MRIread('wmparc.mgz') asegHC=find(aseg.vol == 17 | aseg.vol=53) How would I then replace the data corresponding to the HC labels within wmparc with that of asegHC? Thank you! Jenna ________________________________ From: Jenna Katherine Blujus <jkblujus(a)uwm.edu> Sent: Wednesday, July 8, 2020 5:10 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: Freesurfer Hippocampal Subfield Misalignment Hi Eugenio, Great, thank you! One last question - after I edit the aseg and wmparc files would you recommend that I only rerun the recon-all hippocampal-subfields-T2 step or should I rerun certain autorecon steps of recon-all? Thank you! Jenna Jenna K. Blujus, M.S. Graduate Student Neurobiology of Aging Laboratory University of Wisconsin-Milwaukee jkblujus(a)uwm.edu ________________________________ From: Jenna Katherine Blujus <jkblujus(a)uwm.edu> Sent: Wednesday, July 8, 2020 10:36 AM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: Freesurfer Hippocampal Subfield Misalignment Hi Eugenio, Thank you for the tips! This has happened to a number of my subjects but I have finished editing the HC label in their aseg files. How would I copy the HC from aseg.mgz to wmparc.mgz? Can you clarify what you mean by "you still need to fix the surrounding labels"? Thank you, Jenna Message: 3 Date: Tue, 7 Jul 2020 20:53:12 +0000 From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <85489126-5DC1-4464-810B-01A7E825895A(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Dear Jenna, 1.Manually editing aseg.mgz fixes the initialization (super important). 2.Manually editing wmparc.mgz fixes the intensity priors (less important, but still important) If it?s only 1 subject in a bigger study, I?d probably call it a QC fail and leave it out. If it?s a single case you?re very interested in, I would edit both aseg.mgz and wmparc.mgz (you can copy the hippocampus from one into the other, but you still need to fix the surrounding labels). Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jeigle… Reply Forward Jenna K. Blujus, M.S. Graduate Student Neurobiology of Aging Laboratory University of Wisconsin-Milwaukee jkblujus(a)uwm.edu ________________________________ From: Jenna Katherine Blujus Sent: Tuesday, July 7, 2020 3:23 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Freesurfer Hippocampal Subfield Misalignment Hi Experts, I ran the hippocampal subfield segmentation protocol using a T2 image that does not cover the whole brain in Freesurfer v6.0. I noticed that the alignment of the ?h.hippoSfLabels-T2.v10 output to the anatomical boundaries of the hippocampus in some of my subjects is off. For example, the left hippocampal subfield segmentation in one subject is superior and medial to the hippocampus. I checked the aseg.presurf file (since I am using v6.0) and indeed the whole left hippocampus is off. I saw in a previous thread (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23942.html) that it was suggested to edit the hippocampal segmentation within the aseg file to potentially improve alignment of the subfield segmentation. However, a more recent post (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg54543.html) stated that both the wmparc.mgz and aseg.mgz files would need to be edited and that this was not recommended. Do you have any recommendations on how to move forward? I did edit the hippocampal segmentation within the aseg.presurf file in one of my subjects and reran the subfield segmentation command which substantially improved the output (i.e., it overlays on the hippocampus after correction). Would you suggest that I continue with editing the aseg using previously published protocols on segmenting the hippocampus by hand or would you recommend something else? Thanks in advance! Jenna

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combining left and right pial surface
by Julie Ottoy 10 Jul '20

10 Jul '20

External Email - Use Caution Hi Freesurfer team, I am trying to combine the left and right pial surfaces into one surface. I tried to use the following code: mris_convert --combinesurfs lh.pial rh.pial rh+lh.pial But the outcome is not correct (it has a lot of gaps in the combined pial). Thank you. Best regards, Julie

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mri_glmfit contrast matrix for regression 2 factors 2 levels 2 covariates
by Meaghan Perdue 10 Jul '20

10 Jul '20

External Email - Use Caution Hello, I am running a regression model to test the relationship between cortical thickness and reading ability (wiat word comp) while controlling for sex, scanner (scans obtained at 2 different sites), and age as nuisance variables. I'd like to confirm that I've set up the contrast matrix correctly: 0 0 0 0 0 0 0 0 .25 .25 .25 .25 The first chunk of the y.fsgd file is pasted here for reference: GroupDescriptorFile 1 Title CMI_freesurfer_2020 MeasurementName external Tessellation surface PlotFile /Volumes/Haskins-NC0037-UUGAGE/shares/Research/A223/CMI/flux/flux/lh.gender_age.thickness.10B.mgh DesignMatFile X.mat dods dods DeMeanFlag 1 ReScaleFlag 1 ResidualFWHM 14.975231 LogY 0 Class MaleCBIC Class MaleRU Class FemaleCBIC Class FemaleRU Variables Age wiat_word_comp Input sub-NDARAB348EWRrun-02_new MaleCBIC 5.80538 22 Input sub-NDARAE877NERrun-02_new FemaleCBIC 11.3413 38.5 Input sub-NDARAX277ATUrun-01_new MaleCBIC 16.5465 48.5 Input sub-NDARBK106KRHrun-01_new MaleCBIC 9.69096 33 Input sub-NDARBN620TT7run-02_new FemaleCBIC 15.2318 33 Input sub-NDARCG785NNDrun-01_new FemaleCBIC 9.50479 6 Input sub-NDARCH628LKWrun-01_new MaleCBIC 7.27287 24 Input sub-NDARCW932EU6run-01_new MaleCBIC 9.17842 37.5 Input sub-NDARDA656RBNrun-01_new MaleCBIC 7.07849 16.5 Input sub-NDARDB720VEArun-01_new MaleCBIC 8.95996 16 Thank you! Meaghan -- Meaghan Perdue she | her | hers PhD Student Developmental Psychology Neurobiology of Language University of Connecticut Bousfield A302 Visit my website <https://mvperdue16.wixsite.com/meaghanperdue>

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Re: [Freesurfer] Freesurfer Digest, Vol 197, Issue 7 {Disarmed}
by Ashwati Vipin (NNI) 10 Jul '20

10 Jul '20

External Email - Use Caution Hi Eugenio! Thank so much for your reply. Please find attached the following files you requested: 1. A single subject processed cross sectionally - lh.hippoSfVolumes-T1.v10.txt 2. The same subject process longitudinally - lh.hippoSfVolumes-T1.long.v10.txt Best, Ashwati ________________________________ 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: Friday, 3 July 2020 9:52:43 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 197, Issue 7 Email is from external source. Do not click on links or open files if unsure of sender. Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%… 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. Destrieux atlas volume based in matlab (Gian Marco Duma) 2. Cerebellum segmentation (?lvaro Deleglise) 3. Re: Longitudinal Hippocampal Subfields - negative subfield volume values (Iglesias Gonzalez, Juan E.) ---------------------------------------------------------------------- Message: 1 Date: Fri, 3 Jul 2020 10:42:38 +0200 From: Gian Marco Duma <gianmarco.duma(a)phd.unipd.it> Subject: [Freesurfer] Destrieux atlas volume based in matlab To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CABaZGsdYPOVzFsztFw2ykE0J78vcXQ_RyPz25=C5fety0gZMNQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Dear Freesurfers experts, I need to obtain in the volume and not in the surface, in MNI space with voxels of 2mm. At this moment I do not need to obtain a parcellation of a single subject, even a parcellation in the volume from the MNI template would be great. Do you have any suggestions? thanks

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Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
by Iglesias Gonzalez, Juan E. 10 Jul '20

10 Jul '20

Hi again, First, make a copy of wmparc.mgz, in case something goes wrong. Then: % read aseg aseg=MRIread('aseg.presurf.mgz') % read wmparc wmparc=MRIread('wmparc.mgz') % inpaint hippocampi in wmparc with closes neighboring label wmparc_inpainted = inpaint(wmparc.vol, wmparc.vol == 17 | wmparc.vol=53); % paint your own hippocampi on top wmparc_inpainted(aseg.vol==17)=17; wmparc_inpainted(aseg.vol==53)=53; % write results wmparc.vol= wmparc_inpainted; MRIwrite(wmparc,’wmparc.mgz’); You’ll need the attached function inpaint.m. Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Jenna Katherine Blujus <jkblujus(a)uwm.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Thursday, July 9, 2020 at 21:06 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment External Email - Use Caution Hi Eugenio, Sorry! Can you specify how to copy the edits from aseg to wmparc within Matlab? aseg=MRIread('aseg.presurf.mgz') wmparc=MRIread('wmparc.mgz') asegHC=find(aseg.vol == 17 | aseg.vol=53) How would I then replace the data corresponding to the HC labels within wmparc with that of asegHC? Thank you! Jenna ________________________________ From: Jenna Katherine Blujus <jkblujus(a)uwm.edu> Sent: Wednesday, July 8, 2020 5:10 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: Freesurfer Hippocampal Subfield Misalignment Hi Eugenio, Great, thank you! One last question - after I edit the aseg and wmparc files would you recommend that I only rerun the recon-all hippocampal-subfields-T2 step or should I rerun certain autorecon steps of recon-all? Thank you! Jenna Jenna K. Blujus, M.S. Graduate Student Neurobiology of Aging Laboratory University of Wisconsin-Milwaukee jkblujus(a)uwm.edu ________________________________ From: Jenna Katherine Blujus <jkblujus(a)uwm.edu> Sent: Wednesday, July 8, 2020 10:36 AM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: Freesurfer Hippocampal Subfield Misalignment Hi Eugenio, Thank you for the tips! This has happened to a number of my subjects but I have finished editing the HC label in their aseg files. How would I copy the HC from aseg.mgz to wmparc.mgz? Can you clarify what you mean by "you still need to fix the surrounding labels"? Thank you, Jenna Message: 3 Date: Tue, 7 Jul 2020 20:53:12 +0000 From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <85489126-5DC1-4464-810B-01A7E825895A(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Dear Jenna, 1.Manually editing aseg.mgz fixes the initialization (super important). 2.Manually editing wmparc.mgz fixes the intensity priors (less important, but still important) If it?s only 1 subject in a bigger study, I?d probably call it a QC fail and leave it out. If it?s a single case you?re very interested in, I would edit both aseg.mgz and wmparc.mgz (you can copy the hippocampus from one into the other, but you still need to fix the surrounding labels). Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jeigle… Reply Forward Jenna K. Blujus, M.S. Graduate Student Neurobiology of Aging Laboratory University of Wisconsin-Milwaukee jkblujus(a)uwm.edu ________________________________ From: Jenna Katherine Blujus Sent: Tuesday, July 7, 2020 3:23 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Freesurfer Hippocampal Subfield Misalignment Hi Experts, I ran the hippocampal subfield segmentation protocol using a T2 image that does not cover the whole brain in Freesurfer v6.0. I noticed that the alignment of the ?h.hippoSfLabels-T2.v10 output to the anatomical boundaries of the hippocampus in some of my subjects is off. For example, the left hippocampal subfield segmentation in one subject is superior and medial to the hippocampus. I checked the aseg.presurf file (since I am using v6.0) and indeed the whole left hippocampus is off. I saw in a previous thread (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23942.html) that it was suggested to edit the hippocampal segmentation within the aseg file to potentially improve alignment of the subfield segmentation. However, a more recent post (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg54543.html) stated that both the wmparc.mgz and aseg.mgz files would need to be edited and that this was not recommended. Do you have any recommendations on how to move forward? I did edit the hippocampal segmentation within the aseg.presurf file in one of my subjects and reran the subfield segmentation command which substantially improved the output (i.e., it overlays on the hippocampus after correction). Would you suggest that I continue with editing the aseg using previously published protocols on segmenting the hippocampus by hand or would you recommend something else? Thanks in advance! Jenna

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Lesioned hemisphere
by Alina Rojas 10 Jul '20

10 Jul '20

External Email - Use Caution Hello Freesurfer experts, I’m analyzing subjects with a stroke in one hemisphere. Problem: recon-all breaks and gives an error at the white matter segmentation, what I understand. I don’t need the data from the lesioned hemisphere, I need the cortical thickness from the healthy one. Is there a possibility to only run one hemisphere through freesurfer? Or to project the healthy one on to the lesioned to have an intact brain and run recon-all succesfully? Thanks, Alina

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Label on fsaverage failure
by Eleni Nikalexi 10 Jul '20

10 Jul '20

External Email - Use Caution Dear Freesurfer developers, We have a series of MRI scans and we are trying to extract cortical thickness in certain regions of interest. The ROIs already exist - some are in .img and some in NIFTI format - and we want to tranform them into labels and then register them on fsaverage. The problem is that the ROIs are in MNI152 space (from SPM), with voxel size=2mm. We have tried various commands to register one of the .img ROIs on fsaverage, but they all failed: - $ fslregister --s fsaverage --mov ROI_set1/LeftAnGG.img --reg tmp.dat - $ tkmedit fsaverage T1.mgz -overlay ROI_set1/LeftAngG.img -overlay-reg tmp.dat - $ mri_vol2surf --mov ROI_set1/LeftAngG.img --reg tmp.dat --interp nearest --hemi lh --out Left_AngG_tmp.mgh --projdist-max 0 1 0.1 --noreshape - $ mri_vol2surf --mov ROI_set1/LeftAngG.img --reg tmp.dat --interp nearest --hemi lh --out Left_AngG_tmp.mgh --targ $SUBJECTS_DIR/fsaverage/mri/orig.mgz The result is that the ROI is either not in the right place, or the right size or we just end up with a weird 3D cross shape in freeview. Could you please suggest something that we could do to fix this? Thank you so much in advance! Best regards,Eleni

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