Re: [Freesurfer] Registering Mean Diffusivity to Anatomical Space {Disarmed}

; > I would probably run recon-all on the mni152, and then sample the MD map onto > the mni152 surface, then use mris_apply_reg to map it to an individual. > Also, Thomas Yeo has some possibly-better tools to do this. > > On 5/27/2020 2:02 PM, Nillo, Ryan Michael R wrote: >

[Freesurfer] Registering Mean Diffusivity to Anatomical Space

Hello FreeSurfer users, I have a mean diffusivity map that exists in MNI152 space that I want to register to a subject’s anatomical space. In the end, I want to display the diffusivity on the subject’s surface. I want to ask if this is the correct way to do this: 1) bbregister --s sub-01

[Freesurfer] LGI help

Hello Freesurfer users/developers, I want to run recon-all localGI on a subject who has been processed with Freesurfer 5.3. Whenever I run recon-all -localGI, I always get an error on “make_roi_paths”. There error can be found at the end of this email. I looked at the 5.3 release notes and

Re: [Freesurfer] mri_glmfit ill-conditioned matrix question {Disarmed}

for Precision Neuroimaging Staff Research Associate 1 > On Oct 28, 2019, at 11:17, Greve, Douglas N.,Ph.D. > wrote: > > Yes > >> On 10/28/19 1:04 PM, Nillo, Ryan Michael R wrote: >> Am I correct in assuming this results in z-scoring/normalizing the >> covariates? &

Re: [Freesurfer] mri_glmfit ill-conditioned matrix question {Disarmed}

fsgd: > RescaleFlag 1 > DemeanFlag 1 > > > On 10/26/19 10:45 PM, Nillo, Ryan Michael R wrote: >> Hello, >> >> I ran mri_glmfit with the following fsgd file: >> >> GroupDescriptorFile 1 >> Title CJD >> >> Class MM1_MV1 >> Class MV2_VV2

[Freesurfer] mri_glmfit ill-conditioned matrix question

Hello, I ran mri_glmfit with the following fsgd file: GroupDescriptorFile 1 Title CJD Class MM1_MV1 Class MV2_VV2 Variables frontal Input 7693MV2_VV2 2.930667 Input 11985 MV2_VV2

[Freesurfer] Question on Z-scoring

Hello FreeSurfer users/devs, I have a question on z-scoring. I would like to produce z-scored volume maps for each subject in my study. Is my process correct? 1) mri_surf2surf —srcsubject $sub —trgsubject $sub —sval $sub/surf/$h.volume —tval $sub/surf/$h.volume.mgh —sfmt curv (convert .volume

[Freesurfer] Converting a binary overlay file to label

External Email - Use Caution Hello FreeSurfer users/developers. I manually created a binary overlay file on the pial surface. I am interested in looking at regions outside of this overlay file, so I converted lh.cortex.label to a binary overlay file and took the difference

Re: [Freesurfer] Surfaces with different numbers of vertices. {Disarmed} {Disarmed}

s pial-outer-smoothed create? > > On 7/1/2019 2:33 PM, Nillo, Ryan Michael R wrote: >> Hi Doug, >> >> lh.test.nii was created with: >> >> mri_vol2surf --mov ./misc/lh.probability.nii --trgsubject fsaverage_1 >> --regheader fsaverage_1 --hemi lh --fw

Re: [Freesurfer] Surfaces with different numbers of vertices. {Disarmed}

would have a surface with 73K vertices on fsaverage. >>> Why not use one of the ico representations (40K or 160K vertices)? In any >>> case, mri_surf2surf should do the trick, although you will probably need to >>> create a new subject with a set of 73K vertex surfaces &

Re: [Freesurfer] Surfaces with different numbers of vertices.

have a surface with 73K vertices on fsaverage. Why > not use one of the ico representations (40K or 160K vertices)? In any case, > mri_surf2surf should do the trick, although you will probably need to create > a new subject with a set of 73K vertex surfaces > > cheers > Bruce

[Freesurfer] Surfaces with different numbers of vertices.

Hello Freesurfer users/developers, I have surface with ~73,400 vertices generated from the Freesurfer version 6 fsaverage brain, left hemisphere. I have a surface map that was created by mapping a volume to the fsaverage white surface. Is there a way to map the surface map to the new surface

[Freesurfer] Help for smoothing the pial surface

Hello FreeSurfer users/developers, I want to generate a smooth pial surface similar to the one displayed on the LGI page (https://surfer.nmr.mgh.harvard.edu/fswiki/LGI ) without having to run the entire recon-all process. Additionally, I want to

[Freesurfer] Smoothing the pill surface

Hello FreeSurfer users/developers, I want to generate a smooth pial surface similar to the one displayed on the LGI page (https://surfer.nmr.mgh.harvard.edu/fswiki/LGI) without having to run the entire recon-all process. Additionally, I want to map this surface to the white surface. Is there

Re: [Freesurfer] Projecting subcortical ROI to the cortical surface

mailto:fis...@nmr.mgh.harvard.edu>> wrote: Hi Ryan I don't think projection of that kind of ROI is well-posed. Different parts of it are probably closest to wildly different parts of cortex. What are you trying to acheive? cheers Bruce On Wed, 15 May 2019, Nillo, Ryan Michael R

Re: [Freesurfer] Color scale error

of California San Francisco Department of Radiology and Biomedical Imaging On May 1, 2019, at 12:52 PM, Ruopeng Wang wrote: Can you try turning off/on the scale bar or change the threshold a little bit and see if it updates? Ruopeng On May 1, 2019, at 2:48 PM, Nillo, Ryan Michael R

Re: [Freesurfer] Obtaining stats for a custom label

AM, Nillo, Ryan Michael R mailto:ryanmichael.ni...@ucsf.edu>> wrote: lh.white surface ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Obtaining stats for a custom label

Nillo, Ryan Michael R wrote: External Email - Use Caution Hello Freesurfer developers, I am using the code below to generate the stats table for the ROI. mris_anatomical_stats -l /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/label/rh.custom.label -b subject rh white H

[Freesurfer] Obtaining stats for a custom label

External Email - Use Caution Hello Freesurfer developers, I am using the code below to generate the stats table for the ROI. mris_anatomical_stats -l /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/label/rh.custom.label -b subject rh white However, when I run

[Freesurfer] Projecting a subcortical label to the surface

External Email - Use Caution Hello FreeSurfer users, I have a subcortical segmentation that I want to project to the nearest cortical vertex. Would I use the mri_vol2surf command to accomplish this, or do I need to convert the segmentation into a label, then project the label

[Freesurfer] mri_vol2surf error

External Email - Use Caution Hello FS users, I am having a problem with mri_vol2surf. I want to project subcortical voxels onto the cortical surface. I found out that I can do this with the mri_vol2surf command. I am following the example given on the documentation, but I am

[Freesurfer] Color scale is off

External Email - Use Caution Hello FreeSurfer users, I am using FreeSurfer version 6 with the latest dev version of freeview on a Linux machine. When I load a surface into freeview with a color scale, I notice the scale does not correlate with the values in the surface. The min

Re: [Freesurfer] Setting the origin in native space

Dec 2018, Nillo, Ryan Michael R wrote: >External Email - Use Caution > > Hello FreeSurfer users, > > I want to use the suit software to segment the cerebellum, however the > software requires the origin be set at the anterior composure. I know the > Talairach

[Freesurfer] Setting the origin in native space

External Email - Use Caution Hello FreeSurfer users, I want to use the suit software to segment the cerebellum, however the software requires the origin be set at the anterior composure. I know the Talairach image’s origin is set at the anterior commisure and that there is a

[Freesurfer] Using the SUIT atlas

External Email - Use Caution Hi FreeSurfer users, I am using the SUIT atlas (http://www.diedrichsenlab.org/imaging/suit.htm) to parcellate the cerebellum.To ensure there are no problems with registration, the SUIT pipeline requires that the origin of the input images are

[Freesurfer] Extracting values from a single vertex

External Email - Use Caution Hi FreeSurfer users, I want to extract thickness values at a single vertex. I searched on the support list and found an mris_convert command to use. However, the file I want to extract values from is a volume with multiple frames. When I try to use

Re: [Freesurfer] automating custom color map

:34 PM To: Freesurfer support list Subject: Re: [Freesurfer] automating custom color map I think there is no option to set custom color code for overlay from command-line. I’ll add that option and let you know when it’s ready. Best, Ruopeng On Nov 1, 2018, at 4:51 PM, Nillo, Ryan Michael R

[Freesurfer] Research Opportunity

External Email - Use Caution UCSF, Dept. of Radiology & Biomedical Imaging is seeking a Postdoctoral Scholar for The Laboratory for Precision Neuroimaging We are seeking a postdoctoral candidate with a strong background in genetics human imaging and a desire to use a

Re: [Freesurfer] hippocampal subfield segmentation

ig.cs.ucl.ac.uk/ From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Nillo, Ryan Michael R Sent: Tuesday, August 21, 2018 9:58:25 PM To: Freesurfer support list Subject: [Freesurfer] hippocampal subfield segmentation External Email - Use Caution Hello FreeSurfer

[Freesurfer] hippocampal subfield segmentation

External Email - Use Caution Hello FreeSurfer users, I want to segment hippocampal subfields, but did not have much luck running it. I downloaded the matlab compiler runtime according to this: https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime. Now, there is a directory

[Freesurfer] Thickness measurements.

External Email - Use Caution Hello FreeSurfer experts, I want to use FreeSurfer to generate thickness files using my own surfaces. Is there a way to use white and pial surfaces not generated from the mris_make_surfaces to create thickness files? Mahalo, Ryan M Nillo Staff

[Freesurfer] Longitudinal Processing question

External Email - Use Caution Hello FreeSurfer experts, I have a few questions on the longitudinal processing stream. I am interested in studying longitudinal morphometry changes in a pediatric population. The age range of this population is between 4-20 years with age deltas

[Freesurfer] mri_glmfit question

External Email - Use Caution Hello FreeSurfer Users, I want to run an ROI-based analysis on mri_glmfit as opposed to vertex-based. I know that if I run mri_glmfit with the --table flag and give it the output of asegstats2table or aparcstats2table, it will run the analysis on

[Freesurfer] Hippocampal subfield segmentation error: kvlAutoCrop.bin: command not found

External Email - Use Caution Hello FreeSurfer users, I am trying to run hippocampal subfield segmentation on our subjects on FreeSurfer version 6.0. Unfortunately, I was not able to get very far. I got an error relatively early:

[Freesurfer] Hippocampal subfield segmentation error: kvlAutoCrop.bin: command not found

External Email - Use Caution Hello FreeSurfer users, I am trying to run hippocampal subfield segmentation on our subjects on FreeSurfer version 6.0. Unfortunately, I was not able to get very far. I got an error relatively early:

[Freesurfer] localGI issues

Hello experts, I am using FreeSurfer version 6 and am trying to run recon-all -localGI. Each time I run it, it fails on make_roi_paths. Below is an excerpt of the recon-all.log file. Any help is much appreciated. #@# Local Gyrification Index lh Thu Nov 9 14:06:42 PST 2017 mris_compute_lgi

[Freesurfer] LGI error

Hello FS users, I am using FreeSurfer version 5.3 to calculate local verification index and processing stopped at make_roi_paths. Here, I was given the error below. I searched in the archives and found a solution to the problem was to edit a few lines on SearchProjectionOnPial.m. The new

[Freesurfer] -hemi flag

Hi FreeSurfer users, I am using FreeSurfer v5.3 and have noticed that when -hemi is used as a flag in recon-all, the half I did not specify is not present in wm.mgz. The full command is recon-all -autorecon2 -autorecon3 -hemi (l or r)h -subjid subject_name -sd SUBJECTS_DIR. After running,