Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

ROI analysis, S1, face area
by Eszter Boros 31 Jul '22

31 Jul '22

External Email - Use Caution Dear FreeSurfer Team, I would like to do a ROI analysis focusing on the primary somatosensory cortex (S1) using Freesurfer and see the potential alterations after a (behavioral) treatment . I am wondering how I can do that? First, I picked and looked at the postcentral gyrus and sulcus, but I am specifically interested in the face area. Is there a way to make my analysis more accurate? I am using Freesufer 7.1.1 Thank you for your answer! I greatly appreciate it. All the best, Eszter Boros

1 0

Re: [Freesurfer] Freesurfer Digest, Vol 221, Issue 36
by Jonathan A Winawer 29 Jul '22

29 Jul '22

External Email - Use Caution On Thu, Jul 28, 2022 at 12:00 <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > 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/17A-Eh02HTEIkh0f-xhl-a9F9UFoVcPZ8ScGAVIIkCyX9x… > 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: Understanding ?h.sphere.reg (Salar Dini, Elaheh) > 2. Re: TRACULA -bedp parallel processing (Salar Dini, Elaheh) > 3. Re: ERROR: Talairach failed (Bouchra Guelib) > 4. Problem with hypothalamus subunits? > (Zeng, Victor (BIDMC - Keshavan - Psychiatry)) > 5. Fwd: eTIV (Bouchra Guelib) > 6. Re: mri_jacobian questions (Danielle Carrol) > 7. Re: mri_jacobian questions (Fischl, Bruce) > 8. Applying bonferroni clusterwise correction for 2spaces with > PALM F-contrast (Hye Min Shin) > 9. Re: Problem with hypothalamus subunits? > (Iglesias Gonzalez, Juan E.) > 10. The password request for the Freesurfer VirtualBox Image > (Nina Omejc) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 27 Jul 2022 17:55:33 +0000 > From: "Salar Dini, Elaheh" <elaheh.salardini(a)yale.edu> > Subject: Re: [Freesurfer] Understanding ?h.sphere.reg > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > < > BL0PR08MB467671BB49604E614465BEACF5979(a)BL0PR08MB4676.namprd08.prod.outlook.com > > > > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hi Doug, > > I found the solution to my problem, so please ignore my previous message. > Thanks so much for always helping out anyway. > In case, this question ever comes up for anyone else, here is the solution: > > I just used freesurfer auto-recon steps to create the files I want using > co-registered images. I needed the following files: > > talairach.xfm and rh.cortex.label for my pipeline, so I just the following > steps of recon-all on my co-registered files: > > recon-all< > https://secure-web.cisco.com/1EgFMsGckBYd6kxqV7w3f8yesPKD4GKe7qDUsgWQVhG57f… > > -autorecon1 -subjid <subjid> -talairach< > https://secure-web.cisco.com/13rqQe933ugmKwkEcnA8chHodDfVQwjtWZzI9UaMx6O-BY… > > on post-co-registerated orig.mgz to get talairach.xfm > > > and recon-all< > https://secure-web.cisco.com/1EgFMsGckBYd6kxqV7w3f8yesPKD4GKe7qDUsgWQVhG57f… > > -autorecon2 -subjid <subjid> -white on post-co-registerated > aseg.presurf.mgz, brain.finalsurfs.mgz, wm.mgz, filled.mgz and ?h.orig to > get ?h.cortex.label > > Thanks and all the best, > Ela > > ________________________________ > From: Salar Dini, Elaheh <elaheh.salardini(a)yale.edu> > Sent: Tuesday, July 26, 2022 12:45 PM > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Subject: Re: Understanding ?h.sphere.reg > > Hi Douglas, > It does. Thank you. Can you also help me with something else? If we > coregister bunch of volume and surfaces using the same reg.lta for one > subject, is there a way to safely reflect these changes in label files like > rh.cortex.label or in transformation fies like talairach.xfm? In other > words, can we make any changes to rh.cortex.label and talairach.xfm from > pre co-registeration to make them usable with post co-registration files? > Thanks > > Re: [Freesurfer] Understanding ?h.sphere.reg< > https://secure-web.cisco.com/1UhOk22D0i3wY4fnQeKPgzgZbpFeOxSlca-61id1BOytmB… > > > > Douglas N. Greve< > https://secure-web.cisco.com/16No3VGvLeslOCiSS6roovjBfOQ7EhU19JD6sWi2cufNdr… > > Sun, 24 Jul 2022 19:20:57 -0700< > https://secure-web.cisco.com/19tmADuYKDPqctiaAK489R3GB6vDIWL4rRxkEmP5pU-zA7… > ard.edu%26q%3Ddate%3A20220724> > > > The ?h.sphere.reg xyz coordinates are coordinates on the sphere. To apply > a spherical registration, a point on one spherical mesh is mapped to the > closest point on the other spherical mesh. not sure if that answers your > question ... > ________________________________ > From: Salar Dini, Elaheh <elaheh.salardini(a)yale.edu> > Sent: Thursday, July 21, 2022 5:26 PM > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Subject: Understanding ?h.sphere.reg > > Dear freesurfer experts, > > I was wondering if ?h.sphere.reg files have any coordinates in space > tagged to them? What I actually mean is I'm using TRACULA which itself use > the following files from mri and surf folder (all created by running > recon-all on T1 image): aparc+aseg.mgz, brain.mgz, brainmask.mgz, orig.mg, > T1.mgz and > ThalamicNuclei.v12.Ta.FSvoxelSpace.mgzlh.thickness,rh.thickness,lh.white,rh.white,lh.sphere.reg,rh.shere.reg. > I have all these files (except ?h.thickness and ?h.sphere.reg) in new > coordinates in space created by co-registration. The pipeline we use to > create recon-all results is almost the same as freesurfer pipeline with a > slight difference in autorecon1 step, so the final results are almost > always the same but the coordinate of the brain in 3D space is different, > so we usually end up co-register one's reconstruction result (from our > pipeline) with oneself T1.nii (come from mri_convert T1.dcm) so the > structural mri reconstruction and dwi dcm files are in the same coordinate > and can overlay > . My understanding is that there is no coordinate tagged to ?h.sphere.reg > files in 3D space, rather they are regulatory files which include some > information about x,y,z vertices in regard to the surface of a hypothetical > sphere (and the xyz are coming from the curvature of one's brain). As a > result, I can use ?h.sphere.reg files as they are without any need to make > any changes to match my files after they are coregistered. Is my > understanding correct? > > I'm sorry if my language is not clear enough. I tried my best to describe > the situation, but I'm not sure if my description is clear enough. > > Thank you for your help and time. > Ela >

1 0

Subregion Segmentation of thalamus for TRACULA
by Makenna B McGill 29 Jul '22

29 Jul '22

Hi FreeSurfer Developers, I'm trying to run TRACULA in FreeSurfer v7.3 on OS Monterey. I was unable to download R2014b Runtime on my newer OS, so instead of the segmentThalamicNuclei.sh script, I tried running the newer segmentation tool segment_subregions thalamus ( https://surfer.nmr.mgh.harvard.edu/fswiki/SubregionSegmentation) This was successful, but trac-all looks for the ThalamicNuclei.v12.T1.FSvoxelSpace.mgz file, whereas the subregion segmentation produces the file ThalamicNuclei.FSvoxelSpace.mgz. I'm wondering two things: (1) is the new segmentation tool compatible with trac-all (the wiki says the results will be very close but not identical), and (2) if so, would it be appropriate to rename/link the file so that trac-all can find it, as this user did with the ThalamicNuclei.v13 file ( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg73065.html)? Thank you in advance for any suggestions you might have, and please let me know if anything needs clarified. Best, Makenna *Makenna McGill *(she/her) Doctoral Student in Clinical Psychology University of Texas at Austin

2 2

Problem with hypothalamus subunits?
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 29 Jul '22

29 Jul '22

External Email - Use Caution Hi all, I've downloaded a new dev version of FS 7/19/2022 - and I receive an error with running subunits: mri_segment_hypothalamic_subunits --s 10893/ using 1 thread /mnt/QBERT/freesurfer/python/scripts/mri_segment_hypothalamic_subunits:1023: DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj). * deprecated from version: 3.0 * Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0 volume = np.squeeze(x.get_data()) predicting 1/1 the following problem occured when preprocessing image /..../0893/mri/nu.mgz : 'NoneType' object is not subscriptable resuming program execution segmentation saved in: /..../10893/mri/hypothalamic_subunits_seg.v1.mgz volumes saved in: /..../10893/mri/hypothalamic_subunits_volumes.v1.csv resampled images saved in: /..../10893/mri/hypothalamic_subunits_nu_resampled_1mm.v1.mgz If you use this tool in a publication, please cite: Automated segmentation of the hypothalamus and associated subunits in brain MRI B. Billot, M. Bocchetta, E. Todd, A. V. Dalca, J. D. Rohrer, J. E. Iglesias NeuroImage 2020 Is this a problem with tensorflow? It does not seem clear. No files are actually being written Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

2 3

Amygdala Subfields - longitudinal volumes differ a lot from the cross-sectionals
by Andrea Dell'Orco 29 Jul '22

29 Jul '22

External Email - Use Caution Dear all, I have a Cohort of subjects with multiple time points. I have segmented the T1w with the normal recon-all and sub fields and then with the longitudinal pipeline as described in the wiki. When I compare the sub fields Volumes, there is a good agreement, with the expected variability, between longitudinal and not longitudinal for the Whole Hippocampus rh and lh. The Volumes for the amygdala are on the other hand, really different, especially for the left Whole amygdala. Here some plots with the correlation longitudinal vs non-longitudinal pipeline: https://secure-web.cisco.com/14VEQLZEbs96z59Y5ty9CueQKgO9cELG9hY62vKSTRXY_0… Do someone has some idea, what can be the problem? Regards, Andrea Dell'Orco -- Andrea Dell'Orco Wissenschaftlicher Mitarbeiter Charité – Universitätsmedizin Berlin NeuroCure Clinical Research Center NCRC AG Kognitive Neurologie Charitéplatz 1, D-10117 Berlin Tel +49 30 450 560 185 Fax +49 30 450 7 560 280 Interne Besuchsadresse: CCM, Sauerbruchweg 5, E2 http://secure-web.cisco.com/1ePTkJygSqAcb6M2j8DqUJJZTkIxZCuN07o23jJpGzlCGkh…

3 3

etiv value differs if using recon all vs freesurfer dev
by Miriam Taza 28 Jul '22

28 Jul '22

External Email - Use Caution Hello, I am getting different etiv values when running recon(orange) all VS mri_sclimbic_seg (blue). My analysis uses limbic volumes extracted from the dev version but I am not sure if I should just use the etiv from recon all, given the data is tighter (see attached). Why is there this discrepancy and what do you recommend? [cid:37ebf2b4-95b9-4b28-8fe6-86715ee89d72] Thank you!

2 8

Re: [Freesurfer] Cortical Thickness measures using different ways of processing
by Ariana Fei 28 Jul '22

28 Jul '22

External Email - Use Caution I'm attaching a list of command I used to convert freesurfer cortical thickness output to native space: $Caret5_Command -file-convert -fsc2c "$FreeSurferFolder"/surf/"$hemisphere"h.thickness "$FreeSurferFolder"/surf/"$hemisphere"h.white "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii $Caret5_Command -spec-file-add "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".native.c5.spec surface_shape_file "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii $Caret5_Command -metric-set-column-name "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii 1 "$Subject"_"$Hemisphere"_Thickness $Caret5_Command -file-convert -format-convert XML_BASE64 "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii $Caret7_Command -set-structure "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii $Structure $Caret7_Command -add-to-spec-file "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject".native.wb.spec $Structure "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii $Caret7_Command -metric-palette "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii MODE_AUTO_SCALE_PERCENTAGE -pos-percent 2 98 -palette-name Gray_Interp -disp-pos true -disp-neg true -disp-zero true #cp "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii #commented out GW $Caret7_Command -add-to-spec-file "$T1wFolder"/"$NativeFolder"/"$Subject".native.wb.spec $Structure "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii This already gives negative cortical thickness values in native space. Ariana

2 1

Unsubscribe?
by Archibald, Jessica 28 Jul '22

28 Jul '22

External Email - Use Caution Hi, I signed up last night to send a freesurfer question, but I figured it out. Now I am getting bombarded with emails from this thread and can’t see a ‘unsubscribe’ button. Can you help with this?? Thanks in advance, Jessica Jessica Archibald M.Sc. Kramer Lab- PhD candidate Experimental Medicine ICORD | Blusson Spinal Cord Center 818 W 10th Ave Vancouver, BC, Canada. [UBC E-mail Signature]

2 1

Help with improving the training of an alternative atlas for medial temporal lobe subregions
by Henzen Nicolas 28 Jul '22

28 Jul '22

External Email - Use Caution Hi all, We are aiming at training an alternative atlas of some subregions in the medial temporal lobe using FreeSurfer. As training examples, we manually segmented the subregions using tkmedit and tksurf. In this process we deleted the original segmentation labels around our new regions of interest (see Figure 1). Then, we trained the atlas and parcellated new data as follows: # Train atlases for hemi in lh rh; do mris_ca_train -n 2 \ -t ./doc/LUT.txt \ ${hemi} \ sphere.reg \ CUSTOM_ROIs.annot \ S01 S02 S03 S04 S05 S06 \ ./atlas/${hemi}.CUSTOM_ROIs.gcs done # Create annotations for hemi in lh rh; do for ID in S10 S11 S12 S13; do mris_ca_label \ -orig white \ -novar \ -t doc/ LUT.txt \ ${ID} \ ${hemi} \ sphere.reg \ ${hemi}.CUSTOM_ROIs.gcs \ $SUBJECTS_DIR/${ID}/label/${hemi}.CUSTOM_ROIs.annot done done [cid:image001.png@01D89C87.200FE420]This lead to a very inaccurate parcellation (see Figure 2), also when we filled the unlabeled region with a dummy label (see Figure 3). Figure 1. Example for manual segmentation of the 4 subregions (encircled) with deleted original segmentation labels around. [cid:image003.png@01D8A190.FBE5BED0] Figure 2. Parcellation example using the trained atlas without dummy label for unlabeled regions. [cid:image006.png@01D8A192.42B1DF00] Figure 3. Parcellation example using the trained atlas with dummy label for unlabeled regions. Any comments or suggestions on how to deal with our problem would be greatly appreciated. Many thanks for having taken the time to read and reflect Best, Nicolas

3 2

Cortical Thickness measures using different ways of processing
by Ariana Fei 28 Jul '22

28 Jul '22

External Email - Use Caution Hi, We are recently trying to get cortical thickness from freesurfer and converting them to 32k. A problem we notice is that after converting to 32k, all the cortical thickness values become negative. However, when we load freesurfer thickness files in freeview, everything appears normal. We wonder if merely inverting what we currently have in 32k would be a good idea. Alternatively, we also calculated the Euclidean distance of pial and white after they have been converted into 32k space, which should be cortical thickness. However, when comparing the inverted values and the "pial-white"values, we find that there are some differences. In this case, has anyone ever had similar issues and have suggestions on which one to trust? Thanks! Ariana

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer