Re: [Freesurfer] recon-all clinical : usage with contrast-enhanced T1-weighted images?

Hi Barbara, Yes, you can use recon-all-clinical for the enhanced T1. But, the surface reconstruction might fail and in that case, you might have to try running SynthSR + recon-all. Thank you, Karthik On Jun 13, 2024, at 1:30 AM, Barbara Bellenberg wrote: External Email - Use Caution

Re: [Freesurfer] Probability density function

I'm not sure what you mean, but I don't think we output this information. You can probably do it yourself in matlab or python On 5/21/2024 12:26 PM, Jingjing Liu wrote: External Email - Use Caution Dear Freesurfer team, I am looking for the answer that where I can find the document

Re: [Freesurfer] BIANCA Sensitivity/Robustness to non-brain material in skull-strip

Here on the FreeSurfer list, we don't know much about the FSL tools like BIANCA. Why don't you post to the FSL group? On 6/12/2024 2:51 PM, CRISTIAN MOJICA wrote: External Email - Use Caution Hello, I will be running BIANCA in FSL after some quality control with the requisite files

[Freesurfer] recon-all clinical : usage with contrast-enhanced T1-weighted images?

External Email - Use Caution Dear all, I would like to use the recon-all-clinical pipeline with Gadolinium contrast-enhanced 3D-T1 weighted images. Can you tell me if recon-all-clinical is suitable for this purpose? Thanks in adcance for your support! Barbara

[Freesurfer] BIANCA Sensitivity/Robustness to non-brain material in skull-strip

External Email - Use Caution Hello, I will be running BIANCA in FSL after some quality control with the requisite files to be listed in the Masterfile. I am examining my skull-strip files (in FLAIR space), and most skull strips still have some dura or black space occupied by CSF

Re: [Freesurfer] PETSurfer: pvc'ed and scaled output nifti image

External Email - Use Caution Dear Doug, Thank you for the response. Regards, Sneha From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Wednesday, June 12, 2024 9:11 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL] Re: [Freesurfer]

Re: [Freesurfer] Does motion correction command mc-sess do censoring of high motion timepoints?

In fsfast, the censoring is done in the analysis by creating a tpexclude file and specifying this file when running mkanalysis-sess. Below is a snippet from the mkanalysis-sess --help -tpexclude tpxfilename This is the name of a time point exclude file (TPEF) used for removing outliers in

Re: [Freesurfer] PETSurfer: pvc'ed and scaled output nifti image

It is not PVC corrected. To do that, you'd have to use the --mgx or --rbv Note that doing voxel-wise PVC is tricky because you have multiple tissue types in each voxel. So you can  keep the same resolution but then you have to represent only one tissue type (mgx) or you have to create a higher

Re: [Freesurfer] cluster area from mri_surfcluster and read_curv are inconstant

The lh.area in fsaverage is the area of the white surface (as in an individual subject). But the white surface is not like an individual in that many of the folds have been smoothed out (because it is an average). So mri_surfcluster fixes this internally, which is why you see the discrepancy

Re: [Freesurfer] Help: when will the next version of FreeSurfer become available?

External Email - Use Caution We have no current reports about security issues with the FS release. An address using the string fsbuild will email you directly so you can respond to only that address if you would like to report an issue. Please check you spam folder. PLEASE DO

[Freesurfer] Help: when will the next version of FreeSurfer become available?

External Email - Use Caution Hi, We have been pressured by our IT Security team to address some of the vulnerabilities (e.g., OpenSSL) they found in FreeSurfer 7.4.1. I am wondering if you could share with us when would the next version of FreeSurfer become available? Thanks,

Re: [Freesurfer] Group Stats for hipposubfields, brainstem and amygdalar

Hello Carina, There is a bug in the current implementation of the ConcatenateSubregionsResults.sh script. A patch is now available here and is in the dev branch of FS. The script was incorrectly

[Freesurfer] Does motion correction command mc-sess do censoring of high motion timepoints?

External Email - Use Caution Hi there, I'm using this version of Freesurfer: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 I'm using mc-sess to run motion correction on some functional task and resting state data. I would like to perform censoring on high motion

[Freesurfer] PETSurfer: pvc'ed and scaled output nifti image

External Email - Use Caution Dear team, I am using mri_gtmpvc to obtain PVC'ed regional data which we will use as an input TAC to perform kinetic analysis. In addition, we are also doing static SUVR analysis (sum of frames from 60-90 mins) in which I am scaling input PET data

[Freesurfer] cluster area from mri_surfcluster and read_curv are inconstant

External Email - Use Caution Dear Freesurfer experts, I got the area of a cluster by two methods, and found the results were inconstant. Method 1: During group level analysis, the individual surface was normalized to fsaverage. I exported the cluster area and label file by

[Freesurfer] The Affective Neuroscience Project of the Midlife in the U.S. (MIDUS) study is recruiting a multimodal imaging scientist

External Email - Use Caution The Midlife in the U.S. (MIDUS; https://midus.wisc.edu/) Affective Neuroscience Project Team is excited to bring on an energetic and skilled Ph.D.-level scientist to join our dynamic team and ask questions within the national, longitudinal data to

Re: [Freesurfer] Unequal size groups

We do not offer anything special for this. The difference in group size is not an issue in and of itself. The only problem that would arise is if the groups have different variances. On 5/18/2024 12:07 PM, std...@virgilio.it wrote: External Email - Use Caution Hi I’m using fs-fast

Re: [Freesurfer] Fwd: Atlas Used in FreeSurfer for Segmentation of Fornix, Corpus Callosum, Hippocampus

Mostly these: https://pubmed.ncbi.nlm.nih.gov/15501102/ https://doi.org/10.1016/S0896-6273(02)00569-X For a separate fornix seg, see https://surfer.nmr.mgh.harvard.edu/fswiki/ScLimbic On 5/22/2024 1:34 PM, Ahsan Ali wrote: External Email - Use Caution Hello everyone, Could

Re: [Freesurfer] Intensity affected after using -c flag in mri_convert

The -c means to "conform". In addition to changeing it to 1mm iso, it will change the data type to uchar. Uchar only has 8 bits, so it does an intensity rescaling to make sure all the intensities fit in this range On 5/22/2024 12:55 PM, ERNEST KISSI wrote: External Email - Use

Re: [Freesurfer] Transformed geometry does not match

This usually means that there is a large difference in the geometry between time points eg, the voxel size has changed substantially. If you want  more help, make sure to include the recon-all.log file On 6/7/2024 7:45 AM, Yasmine Salman wrote: External Email - Use Caution Dear

Re: [Freesurfer] Issue with cortical data extraction for mkanalysis-sess

Sorry, I can't understand from you description what is going wrong. How do you know that something is off? Can you list your command lines? On 6/6/2024 8:22 PM, O'Dor, Sarah wrote: We are trying to run resting state connectivity analyses using amygdala ROI. The left hemisphere ran fine, but

Re: [Freesurfer] negative values converting mgz files to nifty

That should have worked, but I would use the method on this page https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat On 6/6/2024 4:07 PM, Nina Rouhani wrote: External Email - Use Caution hello! after freesurfer segmentation (through fmriprep v23), i converted the

Re: [Freesurfer] Bug in mri_convert reslice-like with 4D images

Can you send us the terminal output? Can you point us to the data on the network so that we can recreate? @YH - can you take a look? On 6/6/2024 3:56 PM, Iglesias Gonzalez, Juan E. wrote: Dear FS experts, We get a segfault when I try to resample images with the command: mri_convert

[Freesurfer] INTERNATIONAL CONFERENCE ON ARTIFICIAL INTELLIGENCE IN HEALTHCARE (AIiH)

External Email - Use Caution [apologies for cross-posting] *INTERNATIONAL CONFERENCE ON ARTIFICIAL INTELLIGENCE IN HEALTHCARE (AIiH)* 4 - 6 September 2024, Swansea, UK https://aiih.cc (*2nd CALL FOR ABSTRACT*) Submission deadline: Monday 1 July (FIRM) *1. INTRODUCTION *

[Freesurfer] TRACULA multiple sessions output question

External Email - Use Caution Hello, First of all, thank you for the fantastic software! I have a cohort of individuals with multiple DWI sessions each, and I have been using TRACULA with a configuration file similar to that of Example 3 (“Cross-sectional study, multiple

[Freesurfer] Cannot find mri/transforms/talairach.m3z file

External Email - Use Caution Hello, I am following the longitudinal freesurfer pipeline ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial) and getting this error on the final (LONG) portion: *ERROR: cannot find or read transforms/talairach.m3z* I can

Re: [Freesurfer] Incoporating synthstrip and synthseg into recon-all

This is great to hear! The brain mask of the base is created from the cross runs, and the long runs use the base mask, so you don't need `-synthstrip` for base or long. I believe it's similar for the aseg but you might have to specify `-synthseg` when you run the base - not sure, sorry.

Re: [Freesurfer] Incoporating synthstrip and synthseg into recon-all

External Email - Use Caution To update my progress, I modified my expert.opts file to only contain a single line (*synthstrip --no-csf*) and successfully ran recon-all using the following command: *recon-all -subjid sub-${sub}_ses-${ses} -i /path/to/anat.nii.gz -synthstrip

Re: [Freesurfer] Incoporating synthstrip and synthseg into recon-all

External Email - Use Caution Hi Malte, Thanks for this helpful information. Based on your response, I have a few follow-up questions. 1). Can the expert file (expert.opts) contain a line for the SynthStrip workflow and another line for the SynthSeg workflow, or do I need

Re: [Freesurfer] Incoporating synthstrip and synthseg into recon-all

Hi Dan, I'm afraid these options aren't currently easy to find as they are being parsed by scripts/rca-config. You can find a set of recon-all options along with a description in distribution/etc/recon-config.yaml [1]. To pass additional options to SynthStrip, you'll need to specify an expert

[Freesurfer] Transformed geometry does not match

External Email - Use Caution Dear FreeSurfer developers, I am trying to run longitudinal recon-all -long command. For some subject the recon-all -long command does not work and the error message indicate that 'transformed geometry does not match". I checked and the initial

[Freesurfer] Issue with cortical data extraction for mkanalysis-sess

We are trying to run resting state connectivity analyses using amygdala ROI. The left hemisphere ran fine, but for the right hemisphere, something is clearly off. When we export the results into a table, the unknown column, which should be zero, has values, and one of the regions instead has

Re: [Freesurfer] Bug in mri_convert reslice-like with 4D images

External Email - Use Caution It could help to see the core dump file. If you are on a Mac it will probably display it. If you are on Linux and you have core dumps enabled on the system, then you have to look in the logs. - R. On Jun 6, 2024, at 15:56, Iglesias Gonzalez, Juan E.

[Freesurfer] negative values converting mgz files to nifty

External Email - Use Caution hello! after freesurfer segmentation (through fmriprep v23), i converted the aparc+aseg.mgz file into a nifty file using the below code (freesurfer v7.4.1): -rl $fs_dir/mri/rawavg.mgz -rt nearest $fs_dir/mri/aparc+aseg.mgz

[Freesurfer] Bug in mri_convert reslice-like with 4D images

Dear FS experts, We get a segfault when I try to resample images with the command: mri_convert input.mgz output.mgz -rl reference.mgz when reference.mgz has multiple frames (e.g., a RGB volume). Any idea of why this is happening? Cheers, /Eugenio ( & Pranav)

[Freesurfer] Incoporating synthstrip and synthseg into recon-all

External Email - Use Caution Hello, I am using freesurfer version 7.4.1, and would like to incorporate the recently introduced synthstrip and synthseg functions into my recon-all command, if that's possible. From this archive message (

Re: [Freesurfer] fs_temp_file: Command not found

'fs_temp_file' should be in the same directory as recon-all. Can you check if it exists - 'ls -l $FREESURFER_HOME/bin/fs_temp_file'? Also, '/Applications/freesurfer/7.4.1/subjects' is part of Freesurfer distribution. You should change SUBJECTS_DIR to point to some other directory you have

[Freesurfer] fs_temp_file: Command not found

External Email - Use Caution Hello FreeSurfer developers, I am in the process of learning how to use FreeSurfer and attempting to run the recon-all on FreeSurfer 7.4.1 on a 2019 MacBook Pro (Sonoma 14.5). The response is attached as a pdf, but I have also copied and pasted the

Re: [Freesurfer] Freesurfer license

Hi Liz, Can you try adding a `-B ` to the `singularity run` command? -Paul From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Ayoub, Lizbeth Sent: Monday, June 3, 2024 2:53 PM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer

Re: [Freesurfer] mri_fuse_segmentation error: could not open file

External Email - Use Caution Hello FreeSurfer Developers, I have explored a possible solution to my problem which would include coregistering my fifth scan to the template extracted from the first four scans through the function mri_coreg (described at:

Re: [Freesurfer] Freesurfer license

Thank you Paul, I am using fmriprep-32.1.4.simg, and built it using this command: singularity build ./fmriprep-23.1.4.simg docker://nipreps/fmriprep:23.1.4 I use this command to run fMRIprep: singularity run --nv --cleanenv -B -B -B -B -w --output-spaces

[Freesurfer] fmriprep and freesurfer license

External Email - Use Caution I use this on our HPC: apptainer run --cleanenv --bind ${MRIS}/data:/data:ro --bind ${MRIS}/derivatives/fmriprep:/outputs --bind ${MRIS}/fmriprep_work:/work ${APP} /data /outputs participant --participant_label ${Subject} --fs-license-file

Re: [Freesurfer] Contrast files - 2 groups, 4 covariates

If it is only one subject and you have no continuous variables, you can do it that way. If you have continuous variables, you will need to use DOSS (different-offset same slope) to force the slopes to be the same across classes (because you can't compute a slope from a single data point) On

Re: [Freesurfer] Recon-all for a common template

Why did you do an lr reversal if it looked good? And when you say it looks good, what do you mean. One thing to double check is that the orientation looks ok. Load it in freeview. Up at the top you will see little brain images in coronal, sagital, and axial. When you click on one of those, the

Re: [Freesurfer] How to get the parcellations to the initial space as before running recon all

Does this web site https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat cover what you need to do? On 6/3/2024 10:58 AM, Reji, A. (Amal, Student M-EE) wrote: External Email - Use Caution Hi,     I was trying to get the mesh files for cortical parcellations after running

Re: [Freesurfer] Freesurfer license

Hi Liz, What fmriprep container are you using and what are the full commands that are not working? Are you bind-mounting the freesurfer license file into the container via `singularity exec --bind`? -Paul From: freesurfer-boun...@nmr.mgh.harvard.edu

[Freesurfer] Freesurfer license

Hi, I am using singularity to run fmriprep, and it seems that it is not recognizing the location of my freesurfer license ( it is a new license). I have tried all three options for location, and none work: ERROR: a valid license file is required for FreeSurfer to run. fMRIPrep looked for an

[Freesurfer] How to get the parcellations to the initial space as before running recon all

External Email - Use Caution Hi, I was trying to get the mesh files for cortical parcellations after running recon all. I used the Ernie data set which is the example dataset given by SimNIBS. I did recon all to the

[Freesurfer] Call for applications: LINC fellows program 2024-25

Dear FreeSurfers - Our BRAIN Initiative funded center for Large-scale Imaging of Neural Circuits (LINC) is seeking to name 2 undergrads and 2 postdocs from diverse backgrounds and/or under-resourced institutions “LINC fellows” for 2024-25. The applicants are

Re: [Freesurfer] License for FreeSurfer 5.x

External Email - Use Caution Hello Rafa, If you take a look under,

[Freesurfer] License for FreeSurfer 5.x

External Email - Use Caution Hello everyone, I am working with a neuroimage model that uses the FreeSurfer 5.3 version as preprocessing (only autorecon-I). I have tried to install Freesurfer 5.3, but after reading previous messages in the mailing list It seems the license file

Re: [Freesurfer] Recon-all for a common template

sounds like something is wrong with the image. Did you look at ANTS_QS_... ? Is it oriented correctly? Does it look like a brain in a head? On 5/28/2024 6:07 AM, Chen Yang wrote: > External Email - Use Caution > > Hi everyone, > > I tried to run the reconstruction with the command

Re: [Freesurfer] SynthSR problem

External Email - Use Caution Some commands such as mri_synthsr in previous releases, e.g., 7.4.1, use code built with Intel processor specific instructions that cannot run on an arm processor, i.e., there is not full backwards binary compatibility in that case using the Rosetta

[Freesurfer] SynthSR problem

External Email - Use Caution Hello FreeSurfer developers, I am trying to use mri_synthsr to improve the quality of clinical scans, but this is the error I encountered: Illegal instruction: 4 (I followed the instructions on SynthSR page, using mri_synthsr --i input.nii --o

Re: [Freesurfer] Recon-all for a common template

External Email - Use Caution Hi everyone, I tried to run the reconstruction with the command line: recon-all -i ANTS_QS_template_MNI.nii.gz -subject CGBT -all then I got the error message: talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log

Re: [Freesurfer] Group Stats for hipposubfields, brainstem and amygdalar

External Email - Use Caution If you still have the VM setup on your machine, you can open a new terminal window and then you should see the Freesurfer Environment is setup, FREESURFER_HOME /home/developer/7.2.0/dev FSFAST_HOME /home/developer/7.2.0/dev/fsfast

Re: [Freesurfer] Group Stats for hipposubfields, brainstem and amygdalar

External Email - Use Caution Dear Antoine, Thank you so much again for your reply! I did as you said and it seems like the script is on my computer now, but I get this error: Could not find hipposubfields.rh.T1.v22.txt, skipping subject. For all files. The first few lines

[Freesurfer] freesurfer coordinate systems error: mismatch region hippocampal atlas in matlab and freeview for high resolution

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to acquire the hippocampal subfields and nuclei of the amygdala using a high resolution of 0.333 mm3. However, when comparing the results of using the Freesurfer Coordinate System in matlab, using the

Re: [Freesurfer] MAC compatibilty

External Email - Use Caution The Intel binaries should still run on Silicon Macs using the built-in Rosetta emulation environment. So if you want to use an official release, then the Intel binaries from the most recent June 2023 7.4.1 release can be found here:

[Freesurfer] MAC compatibilty

External Email - Use Caution Good morning, my office needs to buy a new computer and it’s mandatory that it can run free surfer properly. I couldn’t really find definitive informations about the compatibility with latest Mac machines with M2-M2pro-M3 processors. Since I always

[Freesurfer] Research Technician positions in the FreeSurfer lab

Hi everyone, If you or anyone you know is looking for entry-level Research Technician positions working with FreeSurfer and/or postmortem human brain MRI research, please feel free to check out or share some of the job openings in our lab: https://lcn.martinos.org/jobs/ We are also looking for

[Freesurfer] squirrel data sharing format available in beta

External Email - Use Caution The squirrel data sharing format is now available in beta format and we're looking for public comment. The squirrel format is designed to use the minimum number of objects to describe all parts of neuroimaging analysis. From experiments and raw data to

[Freesurfer] run_samseg: Optimizer: maximalDeformation is too small; stopping; killed

External Email - Use Caution Hi Marie, The error message "Killed" is usually thrown when the device runs out of memory. Can you double-check that this is not the case? If you're on Ubuntu you can track your memory usage with the command ("htop" or "top"). The SAMSEG log you

[Freesurfer] run_samseg: Optimizer: maximalDeformation is too small; stopping; killed

External Email - Use CautionHello Freesurfer Developers,    I'm a medical student training with Freesurfer for my doctor thesis. My goal is to measure the brain volumetry of patients via SAMSEG. Attached is my logfile for run_samseg.      When i run the samseg command:   

[Freesurfer] Fwd: Atlas Used in FreeSurfer for Segmentation of Fornix, Corpus Callosum, Hippocampus

External Email - Use Caution Hello everyone, Could anyone please help me to know which Atlas is used in the segmentation of corpus callosum, hippocampus, and fornix using freeSurfer from Brian MR images. I have gone through the literature but couldn't find it. With Regards Ahsan

[Freesurfer] Intensity affected after using -c flag in mri_convert

External Email - Use Caution Dear fresurfer team, Why does the use of conform flag (-c) in mri_convert affect the intensity of the image? I have an image with absolute intensity of 1000 and after using the conform flag in mri_convert, the intensity is around 98.1. why is there

Re: [Freesurfer] Atlas Used in FreeSurfer for Segmentation of Fornix, Corpus Callosum, Hippocampus

Mostly these: https://pubmed.ncbi.nlm.nih.gov/15501102/ https://doi.org/10.1016/S0896-6273(02)00569-X cheers Bruce From: Ahsan Ali Sent: Wednesday, May 22, 2024 4:31 AM To: Freesurfer support list ; Huang, Yujing ; Fischl, Bruce R.,PHD Subject: Atlas Used in FreeSurfer for Segmentation of

Re: [Freesurfer] fspalm error

External Email - Use Caution I have the same error that doesn't resolve with --mgh or mgz. warning: excluding contrast file /Volumes/mnu/MRI/XXX/NIFTI/FreeSurfer/rs-fMRI_AROMA/G3V0_Comparison/fc.MDseed.surf.rh/MD/G3V0_PALM.glmdir/group.effect/C.dat since it has multiple rows

[Freesurfer] Atlas Used in FreeSurfer for Segmentation of Fornix, Corpus Callosum, Hippocampus

External Email - Use Caution Dear FreeSurfer Team, After reviewing the literature, I have a question: which atlases are used in the segmentation of the fornix, corpus callosum, and hippocampus from magnetic resonance images using FreeSurfer? This is a significant question for me,

[Freesurfer] PhD candidate position - high-resolution imaging of the human claustrum

External Email - Use Caution Dear colleagues, I would greatly appreciate if you could forward this job announcement to potentially interested candidates. The Visual Neuroscience Lab (PI: Natalia Zaretskaya) at the Institute of Psychology, University of Graz jointly with the

[Freesurfer] Probability density function

External Email - Use Caution Dear Freesurfer team, I am looking for the answer that where I can find the document of Probability density function in voxels of each brain volume after preprocessing. Because I need these indicators. Thank you so much in advance for your reply!

[Freesurfer] Group Stats for hipposubfields, brainstem and amygdalar

External Email - Use Caution Dear Freesurfer team, I am looking for a group stats command like the asegstats2table and aparcstats2table command for hipposubfields, brainstem and amygdalar, but I couldn’t find it in the archives. I remember it was mentioned in the recent

[Freesurfer] how to resolve recon-all stopping at fill step

External Email - Use Caution Dear FreeSurfer developers, Apologies for emailing once again about how to resolve the recon-all stopping exactly at the fill step. I understand this may have to do with specific issues on UCSD's computer cluster, but if UCSD's cluster is not having

[Freesurfer] Request to Edit Page (if possible)

External Email - Use Caution Hello, I hope all is great. I ran into many issues using the -make flag with V 7.1 (based on instructions found in

[Freesurfer] Freesurfer on a high-performance cluster (HPC) - MATLAB runtime

External Email - Use Caution Hi all, I hope your weekend is going great! *Context*: I am trying to run the amygdala/hippocampus segmentation in an hpc. *Issue*: The cluster that I use doesn't have the libmwlaunchermain.so file from MATLAB's 2019b runtime under

[Freesurfer] Unequal size groups

External Email - Use Caution Hi I’m using fs-fast to map the connectivity differences between 3 groups. My problem is unequally sized groups. In the sense that the first group consists of 40 subjects, the second of 190, and the third of 18. What solutions does FreeSurfer

[Freesurfer] mri_watershed Error: read failed

External Email - Use Caution Dear Freesurfer developers, I am currently conducting a research project in which I am running 7T MP2RAGE images in Freesurfer version 6.0.1 but have a run into an issue. For 3 images I receive a watershed error stating “mri_watershed error: GLOBAL

[Freesurfer] Valid options.txt file for mris_pmake (and maybe .dsh.yml too)

External Email - Use Caution Hi list! I was reading the documentation on mris_pmake (by the way, it is outdated, the documentation still asks for --surface00, at least in 7.3.2), and I would like to have a valid options.txt file to make it work with dsh (a valid example .dsh*.yml

Re: [Freesurfer] Issue related to converting .nii.gz file to .mgz using FreeSurfer's mri_convert

I'm trying to understand the issues related to mri_convert. It looks like you did the following: 1. mri_convert aparc.DKTatlas+aseg.deep.mgz aparc.DKTatlas+aseg.deep.nii.gz 2. saved the manually edited as aparc.DKTatlas+aseg.deep.edited.nii.gz 3. mri_convert aparc.DKTatlas+aseg.deep.edited.nii.gz

Re: [Freesurfer] error using mri_em_register

There is an error in your first 'recon-all -autorecon1 -noskullstrip' attempt: " \n ERROR! FOV=302.000 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. \n " You can't

[Freesurfer] error using mri_em_register

External Email - Use Caution It does not create the nu.mgz file. Error logs are attached. The result is that when running recon all it cannot find the LH and RH files and then collapses. Darwin Kernel Version 21.3.0 iMac-Pro 21.3.0 Root: xnu-8019.80.24~20/RELEASE_X86_64 x86_64

[Freesurfer] Issue related to converting .nii.gz file to .mgz using FreeSurfer's mri_convert

External Email - Use Caution Hello FreeSurfer Developers, I am using FastSurfer for this processing, but the issue is related to FreeSurfer's mri_convert function. I wanted to perform some manual segmentation edits on the "aparc.DKTatlas+aseg.deep.mgz" output file of

Re: [Freesurfer] Hippocampus subfield LUT

Look in $FREESURFER/FreeSurferLUT.txt This has those indices (and a lot more). If you want just the hippo SF indices, you can run something like mri_segstats --seg hipposf.mgz --ctab-default --sum sum.dat The indices will be in sum.dat On 5/14/2024 11:04 AM, karl landheer wrote:

[Freesurfer] Hippocampus subfield LUT

External Email - Use Caution Hello, I am looking for the LUT which converts the indices in images like lh.hippoAmygLabels-T.v22.mgz to region name. Is this available anywhere? I can’t find it ___ Freesurfer mailing list

Re: [Freesurfer] Retinotopy error computing contrast matrices

External Email - Use Caution Hello Freesurfer Experts, I find a way to do the analysis solving the contrast matrices problem, but I am not sure about this solution, mostly because the results don't look correct to me. So basically my solution was replicate my 3 runs, and the

[Freesurfer] Harmonization (Site/Scanner) for FreeSurfer Area Data

External Email - Use Caution Hi FreeSurfer experts, I have harmonized across site and scanners on both thickness and area for a large cohort (500+ subjects). We are seeing high covariance values when comparing the harmonized and non-harmonized area datasets and trying to

[Freesurfer] Subcortical surfaces from volume features.

External Email - Use Caution Dear Freesurfer Experts, I am looking into generating subcortical surfaces from the subcortical volumes generated from recon-all. The reason for this is I am trying to create a vertex based Morphological Similarity Network generated from both

Re: [Freesurfer] Contrast files - 2 groups, 4 covariates

External Email - Use Caution Thank you Douglas. That’s much clearer. I do however, have a subject without a gender disclosure. Would I set up my class and contrasts as: 5 classes: PatentientsMale, PatientsFemale, HCMale, HCFemale, HCNa then use contrast [0.5 0.5 -0.33 -0.33

Re: [Freesurfer] Contrast files - 2 groups, 4 covariates

The first one will test for a difference between group offset/intercept accounting for age, gender, episodes, and residuals. By setting a regressor contrast element to 0, one accounts for that variable because the variable appears in the model that is fit to the data (and so its effects

[Freesurfer] mri_segment_hypothalamic_subunits 7.4.1 issue

External Email - Use Caution Dear FreeSurfer developers, I have just tested the Segmentation of hypothalamic subunits, but unfortunately it does not work. I simply wrote: mri_segment_hypothalamic_subunits --s subject_folder or mri_segment_hypothalamic_subunits --s

[Freesurfer] Contrast files - 2 groups, 4 covariates

External Email - Use Caution Hello! I am having trouble with creating my contrast files. I did go over FsfdExamples

Re: [Freesurfer] MCR install for parcellation

External Email - Use Caution Hello Antonio, With the 7.4.1 release, you can install R2014b or R2019b matlab runtime environment into the freesurfer tree. Earlier freesurfer releases use R2014b. I would setup the freesurfer environment first, and then pass in the value of

[Freesurfer] MCR install for parcellation

External Email - Use Caution Messers FreeSurfer developers, I dowloaded MCR zip file for linux in /home/vboxuser/Downloads from MatLab website. I extracted files in new foldern named Matlab_Component_Runtime_R2014b in Downloads. I am trying to install Matlab Component Runtime,

[Freesurfer] Postdoc Positions in Cognitive Neuroscience/ Neuroimaging Genomics

External Email - Use Caution Postdoc positions are available at Zhejiang University (Hangzhou, China). The successful candidates are expected to work on multi-disciplinary projects in cognitive neuroscience, neuroimaging and computational modelling related to individual

[Freesurfer] Incorporating hi-res T2w image in longitudinal pipeline

External Email - Use Caution Good afternoon, We are collecting hi-resolution T1w and T2w images (0.8mm3) in a pre-/post- design. I am using Freesurfer 7.4.1 to process the data and have been successful in ingressing the T2w images in the cross-sectional recon-all runs with -T2

Re: [Freesurfer] outcome directions of longitudinal two stage model

External Email - Use Caution Yes, I was wrong in considering tp1 - tp2 or tp2 - tp1. Actually, my question is: If the changing rate or % in thickness of a region calculated using long_mris_slopes is a positive number, does that mean it's an increase in thickness from baseline (or

Re: [Freesurfer] surface and cortical thickness normalization

The reason I suggested scaling by eTIV is an analogy with a box of paper. The surface area of the paper in the box scales linearly with the volume in the box (twice the volume, twice the paper, twice the area). I vaguely remember doing a test of this, but, if I did, it has been a while.

Re: [Freesurfer] Difference between 2 ways to set up fsgd file and contrasts

They are not identical, for  sure. In general, I discourage people from modeling categorical variables (eg, Group1/2 below) as continuous variables because you make assumptions that might not be reasonable (eg, females will have twice the thickness as males). I would use the first method. On

Re: [Freesurfer] outcome directions of longitudinal two stage model

not sure what you mean and/or referring to. can  you elaborate? On 5/7/2024 4:03 PM, L wrote: External Email - Use Caution Dear exports, I am wondering whether the outcomes of the longitudinal two stage model is tp1 - tp2 or tp2 - tp1. Thank you, Lihong Wang -- - Lihong

Re: [Freesurfer] recon-all process still not finishing properly

It should just run the fill step. However, I've been slowly reprogramming recon-all to just see what needs to be run and rerun it, so you might get more than just the fill. On 5/3/2024 4:38 PM, Dong, Yilei wrote: External Email - Use Caution Hi Freesurfer Developers, Just to reply

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