Freesurfer July 2020

freesurfer@nmr.mgh.harvard.edu

96 participants
160 discussions

Re: [Freesurfer] aparcstats2table error
by Devika K 15 Jul '20

15 Jul '20

External Email - Use Caution I tried doing cortical parcellation using Destrieux atlas. I ran the aparcstats2table command from the SUBJECTS_DIR directory containing all of the output from recon-all. But I got an error, PFA. Do I need to run any other commands before running aparcstats2table command, I would be grateful if anyone could help me to resolve this issue. Many thanks in advance. Regards Devika K Research Scholar, Dept of EEE e: k_devika(a)cb.students.amrita.edu Amrita Vishwa Vidyapeetham Coimbatore, India

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Segmentation with FreeSurfer 7.1
by Sara PONTICORVO 15 Jul '20

15 Jul '20

External Email - Use Caution Dear FreeSurfer experts, we are performing some morphometric analyses using the new FreeSurfer 7.1 and we have encountered some large segmentation problems, mostly in the occipital pole. You can find some example images attached to this email. As the raw data do not present any particular problem, we selected the subject with the worst errors and performed, on the same workstation, the recon-all procedure using the old FreeSurfer 6. We noticed that the segmentation obtained with FreeSurfer 6 is good and does not present any particular defects. Do you have any clue on why there are these discrepancies between the two versions? Thanks a lot, Sara -- Sara Ponticorvo PhD Student Departement of Medicine Surgery and Dentistry, University of Salerno

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Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
by Iglesias Gonzalez, Juan E. 14 Jul '20

14 Jul '20

Hard to tell, Jenna! Please do upload a sample subject using the instructions in the wiki, and I’ll take a look. 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: Tuesday, 14 July 2020 at 13:15 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, I might have fixed this particular issue. I ran AFNI's 3dUnifize on the T1 before submitting it to recon-all and this improved the segmentation (it now overlays on the hippocampus). However, I still have some other files that this solution did not work for (see attached picture). I have a few subjects where the segmentation is slightly superior to the hippocampus. Editing the aseg or running 3dUnifize did not fix this issue. Do you have any suggested solutions? Thank you for your help! Jenna

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Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
by Iglesias Gonzalez, Juan E. 13 Jul '20

13 Jul '20

Hi Jenna, Would it be posible for you to share the subject? This is very weird. 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: Monday, July 13, 2020 at 19:29 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, I reran the segmentations after editing the aseg.presurf.mgz files and copying the edited HC to the wmparc.mgz files but the segmentations did not improve. Is there anything else you would suggest to do? Here is an example of one of my subjects. As you can see the left segmentation is not aligned with the left hippocampus. Thanks, Jenna

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Re: [Freesurfer] QAtools with Freesurfer version 6.0
by Hoopes, Andrew 13 Jul '20

13 Jul '20

Hi Kamy, The QA tools are actually developed outside of our lab. It might be helpful to contact the Reuter lab directly - https://github.com/Deep-MI/qatools-python best Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Wakim, Kathryn-Mary" <KathrynMary_Wakim(a)urmc.rochester.edu> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Thursday, July 9, 2020 at 7:51 PM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] QAtools with Freesurfer version 6.0 External Email - Use Caution Hi all, I’m relatively new to Freesurfer, and I am just beginning to check the output of my recon-alls using QAtools. However, I’m running into a number of difficulties and errors with QAtools, and I’m wondering if this tool is not yet optimized for the current version of Freesurfer. I have attached the recon_checker.All.summary.log output from QA tools. Below, I’ve also highlighted some of the errors and issues I see in the recon_chcker log file. Please note thatt, per the subject’s recon-all log file, recon-all ran to completion with no errors. Overview of recon_checker errors: 1) ERROR: Subject 10201003 missing output file ../mri/nu_noneck.mgz * Note: this is repeated for a number of different output files 2) ERROR: Recon-all steps missing in subject 10201003 status file 3) View your snapshots by opening this file in an internet browser: * Note: I have attached a screenshot of the output .html file in-browser. Note that I have installed and verified installation of ImageMagick. Thank you very much for your help, Kamy Wakim

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Dockerized version of Freesurfer 7.1
by Morgan Botdorf 13 Jul '20

13 Jul '20

External Email - Use Caution Hi Freesurfer Team, I am working on running recon-all on a large dataset using AWS. I saw that there is a dockerized version of Freesurfer 6.0. However, I would like to use Freesurfer 7.1. I was wondering if you could give me any information on whether there is (or will be) a dockerized version of Freesurfer 7.1? I appreciate any information you can provide! Thank you, Morgan Morgan Botdorf, M.S. Doctoral Candidate Neurocognitive Development Lab University of Maryland, College Park mbotdorf(a)terpmail.umd.edu Office: 301.405.5922

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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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Freesurfer July 2020