Re: [Freesurfer] Hypothalamus segmentation output

External Email - Use Caution Perfect! Thank you so much for the clarification. Stay safe On Tue, Mar 16, 2021 at 11:53 PM Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mgh.harvard.edu> wrote: > Dear Alex, > > As explained in the wiki, if you run the module on a FreeSurfer

Re: [Freesurfer] Hypothalamus segmentation output

Dear Alex, As explained in the wiki, if you run the module on a FreeSurfer processed subject, the output will be in the subject’s mri directory, and will be called: hypothalamic_subunits_seg.v1.mgz So you could run something like: cd $SUBJECTS_DIR//mri freeview nu.mgz

[Freesurfer] Hypothalamus segmentation output

External Email - Use Caution Dear Freesurfer experts, Hope that you all are well and stay safe. I would like some help figuring out the code to open the output for the hypothalamus segmentation (via freeview). Does anyone have this info? I didn't find it on the website. Thank

Re: [Freesurfer] Meylin overlay

External Email - Use Caution There is a bug in Freeview, I believe it has been fixed in the dev build. Matt. From: on behalf of バキット・ムダシル Reply-To: Freesurfer support list Date: Tuesday, March 16, 2021 at 10:38 PM To: Freesurfer support list Subject: Re: [Freesurfer] Meylin

Re: [Freesurfer] Meylin overlay

External Email - Use Caution Thanks Matt. I tried it with version 7.1.1 of freesurfer didn’t work but worked fine with freesurfer 6. With version 7.1 it failed to load the gii file. Any idea how to fix it? Mudathir > On Mar 16, 2021, at 21:08, Glasser, Matthew wrote: > >

Re: [Freesurfer] Aseg missing frontal portions - subcortical okay?

External Email - Use Caution Okay, thank you very much! From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Tuesday, March 16, 2021 11:03 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Aseg missing

Re: [Freesurfer] Matlab Runtime error line 334

Hi Matt, Hopefully this isn’t specific to M1, but I’m not sure it would be in this case. Maybe try running fs_install_mcr with sudo in front? Some users are suggesting it here: https://www.mathworks.com/matlabcentral/answers/176228-error-message-install_unix-not-found best Andrew From:

Re: [Freesurfer] freesurfer install error

External Email - Use Caution It reads like you are trying to install on an Ubuntu system, e.g., Ubuntu 18 or Ubuntu 20? On Ubuntu you can try the install command,$ sudo apt installlibjpeg62 Also it would be good to know what freesurfer release you are installing, e.g., 7.1.1.

Re: [Freesurfer] Putamen and claustrum

Hi Donatas, did I write that? I don't remember how it works. I think it is just some minor mechanical clean up. doug On 3/16/2021 12:37 PM, Donatas Sederevicius wrote: External Email - Use Caution Dear FreeSurfers, I had a look at the RB_all_2020-01-02.gca atlas and there was no

Re: [Freesurfer] Help

We don't have a lobar segmentation. You can get whole cerebellum (GM and WM) from our standard analysis (recon-all) or using samseg. On 3/5/2021 3:27 PM, Murray Howerth wrote: > External Email - Use Caution > > I am new to this platform and would like some direction as how to obtain >

[Freesurfer] Putamen and claustrum

External Email - Use Caution Dear FreeSurfers, I had a look at the RB_all_2020-01-02.gca atlas and there was no probabilistic information regarding the claustrum. However, in the mailing archive I have found the following: "On 2 May 2017, at 17:57, Douglas Greve wrote: […]

Re: [Freesurfer] make_average_subject error

What command are you using? make_average_subject? Send the command line and terminal output On 3/10/2021 3:53 PM, Jordan Mullins wrote: External Email - Use Caution Hello, I am trying to create an average subject from a set of subjects, but keep getting an error that says

Re: [Freesurfer] Flip image (resize)

You should contact SPM On 3/10/2021 11:57 AM, Ramesh Babu wrote: External Email - Use Caution Dear Experts, The fMRI data, when viewed in SPM, some images have 3x3x4 voxel dimensions and some images have -3x3x4. Should I flip the image (using resize option) so that all images will

Re: [Freesurfer] Absolute volume difference between Freesurfer 6.0 and 7.1

I'm not sure where the differences are coming from, but it sounds like the range we are seeing. My guess is that the intensity normalization changes are the cause. There are always voxels on the edge of a structure that are ambiguous, and a slight change in intensity can cause their

Re: [Freesurfer] editing surfaces in two different Freesurfer versions

Yes, you should be able to run 7.1 recon-all on 5.3/6.0 and it should respect the edits (but make a copy before you do!) On 3/9/2021 6:59 PM, Lara Foland-Ross wrote: > External Email - Use Caution > > Hi there, > > We are making the switch to Freesurfer v7.1 and wondering - can we

Re: [Freesurfer] Troubleshooting: Soft Failures

Can you send the recon-all log file? On 3/9/2021 2:06 AM, 崔鹏程 wrote: External Email - Use Caution Hi FreeSurfer experts, Recently, I used Fresurfer's */recon-all/*toprocess our own T1 MRIbrain volumes which is 0.7 m3 isotropic.For most young brain cases, FS performs very well, the

Re: [Freesurfer] Aseg missing frontal portions - subcortical okay?

Then it is probably ok On 3/8/2021 1:46 PM, Laurel Quinlan wrote: External Email - Use Caution The subcortical structures do look okay to me. -Laurel *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of

Re: [Freesurfer] Failed tissue type check {Disarmed}

I don't know. Can you upload the data so I can take a look? Instructions are below. I'd need both the anatomical data (output of recon-all) and input.nii.gz and PET.lta From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now

Re: [Freesurfer] Problem with freesurfer measures

I think they will give very similar results, but my guess is that #1 is a little better On 3/8/2021 11:40 AM, Alberto Del Cerro Leon wrote: External Email - Use Caution I want to use the annotation file created by myself in fsaverage to calculate the anatomical stats, but i dont 

Re: [Freesurfer] Cortical surface analysis

On 3/8/2021 11:38 AM, Ornaith O Reilly wrote: External Email - Use Caution Hello Freesurfer developers, I am new to Freesurfer and I'm hoping that someone can help me. My goal is to be able to visualise electrodes contacts that are on lying on the cortical surface on a flat map

Re: [Freesurfer] Using Aseg atlas/subcortical segmentation with T2 MRI

There are several things you can try. First, you can use samseg instead of recon-all to generate the subcortical segmentation. Samseg works on any modality or combination of modalities. Second, you can try to build and apply your own atlas. This is more difficult, but you would start with

Re: [Freesurfer] mri_surf2surf command error

Can you give the command line that is failing and the terminal output? On 3/4/2021 12:53 AM, 1248742467 wrote: ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution Hello, Fs I want to template some subject to fsaverage5, but now I meet some problems FreeSurfer version: Fs6 Download

Re: [Freesurfer] Two questions about FDR correction

On 3/3/2021 3:45 PM, Funk, Quentin wrote: External Email - Use Caution Freesurfer experts, I have two questions that probably show my lack of understanding of many things related to thickness comparisons. I have a group of controls and a single subject with pathology. I'd like

Re: [Freesurfer] Recon-all Ending Fast

Hi Akila You haven't told it to do anything, so all it does is create the directory structure and import the data. You need to add a directive like "- all" to the recon-all command line Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of A.R. Sekar Sent: Tuesday, March

Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?

Thanks, Franziska. It seems to be a problem with partial voluming. Cerebral white matter (white pixels) mixes with a thin layer of cerebrospinal fluid (black pixels) and the result is a bunch of gray pixels that look like the pulvinar. Partial voluming is one of the biggest problems with these

Re: [Freesurfer] license file not working

Hi Philipp, Okay interesting. So it's failing on centos 8. Do you mind sending the license file directly to my email (off-list)? thanks Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Saemann, Philipp Sent: Monday, March 15, 2021

Re: [Freesurfer] Meylin overlay

External Email - Use Caution You should be able to load files like ${StudyFolder}/${Subject}/MNINonLinear/Native/${Subject}.${Hemisphere}.MyelinMap[_BC].native.func.gii in Freeview. Matt. From: on behalf of バキット・ムダシル Reply-To: Freesurfer support list Date: Monday, March

[Freesurfer] Recon-all Ending Fast

External Email - Use Caution Hello, I am trying to run the recon-all function and the whole process is completing within a minute or so. I was told that the whole process would take between 6-24 hours. This is the output I am getting after entering the command:

[Freesurfer] freesurfer install error

External Email - Use Caution Hello, Fs After installing FreeSurfer, use tkregister2, tkmedit, tkurfer, and recon all -- help to verify whether the installation is successful. The first and fourth commands are OK, but the second and third commands display the same error: glut:

[Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?

External Email - Use Caution Dear Eugenio, here are the zipped norm.mgz and automated segmentations for two subjects: