Freesurfer

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30080 discussions

Saving ROIs on freeview
by Tina Thomas 24 Jun '21

24 Jun '21

External Email - Use Caution Hello, I am attempting to edit ROIs using Freeview, but when I save the label files, none of my edits are being saved. I am using a Mac. When I tried troubleshooting on a different computer (PC), I was able to save changes using the same methods. Could this be an issue with the version of Freesurfer (I'm using 6) or the computer I'm using? Is there another way to work around this issue? I also had an issue where when I used Freeview buttons to load an ROI, it wouldn't work unless I did it using code. Please let me know if this is something you have seen before or if you can help with this issue! Thank you, -Tina

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Longitudinal processing
by AJ 24 Jun '21

24 Jun '21

External Email - Use Caution Hi, After running longitudinal processing and creating base and long runs, When looking at volumes of various structures over time of the same subject, are the volumes not need to be corrected by eTIV since head size does not vary overtime? Many thanks for your input. Sincerely, AJ

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Fwd: Running FreeSurfer with fmriprep
by Rosalia Dacosta Aguayo 24 Jun '21

24 Jun '21

External Email - Use Caution Dear Freesurfer's experts, I have run recon-all all to one subject with fmriprep. The work finished without errors. However, after inspecting the results, I have seen that there are some *grey regions* (mainly frontal and temporal ones) that have not been fully covered. I wonder how I could proceed in order to improve the segmentation. Kind regards, Rosie

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Is hypointensities part of lh/rh cerebral white matter from aparc+aseg.mgz using mri_segstats
by miracle ozzoude 24 Jun '21

24 Jun '21

External Email - Use Caution Hello All, I was wondering if the Right/Left-Cerebral-White-Matter in the aparc+aseg.mgz contains WM hypointensities. mri_segstats --seg aparc+aseg.mgz -i dti_fa.nii.gz --sum dti_fa.stats --ctab FreeSurferColorLUT.txt Best, Paul

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Visualization of specific ROIs
by Jennifer James, MD 24 Jun '21

24 Jun '21

External Email - Use Caution Hello, We used FreeSurfer version 6.0 to extract thickness values and then used SPSS for statistical modeling. We found significant results in the thickness of the following two regions: *lh_G&S_cingul-Mid-Ant_thickness* *lh_S_front_middle_thickness* We want to make a simple figure showing just these two areas of the brain for visualization purposes only (similar to the attached figure). Could you let us know how we can make such an image in Freeview? Any help is highly appreciated! Best, Jennifer

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Seeing "Include the flag -cw256 with recon-all!" for HCP 7T data
by Soichi Hayashi 24 Jun '21

24 Jun '21

External Email - Use Caution Hello. I am having a problem running freesurfer on a HCP 7T data and I am wondering if someone from this mail list could help me out. I am trying to run freesurfer (v7.1.1) and I am seeing the following error message. **************************************** ERROR! FOV=268.800 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. **************************************** I am already passing -cw256 option. $ recon-all -i ../60ccadb32b8bed7302843abc/59a09e1d34ea2464e4d1bdcd/t1.nii.gz -subject output -all -parallel -openmp 8 -hires -cw256 -expert expert.opts The error message sounds like my -cw256 option is ignored, but I am not sure.. I see this at the top of the stdout log. INFO: hi-res volumes are conformed to the min voxel size Subject Stamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 Current Stamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 INFO: SUBJECTS_DIR is /export/prod/60ccadb32b8bed493f843abb/60ccadbb2b8bed6894843ac0 Actual FREESURFER_HOME /usr/local/freesurfer Linux slurm9-compute3 4.15.0-126-generic #129-Ubuntu SMP Mon Nov 23 18:53:38 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux '/usr/local/freesurfer/bin/recon-all' -> '/export/prod/60ccadb32b8bed493f843abb/60ccadbb2b8bed6894843ac0/output/scripts/recon-all.local-copy' -cw256 option is now persistent (remove with -clean-cw256) /export/prod/60ccadb32b8bed493f843abb/60ccadbb2b8bed6894843ac0/output I believe "-cw256 option is now persistent" means that freesurfer is aware that I am setting this parameter? expert.opts is empty. I appreciate if you could assist me in troubleshooting this error message! Soichi

2 1

Demeaning for Longitudinal Analyses
by WON JONG CHWA 24 Jun '21

24 Jun '21

External Email - Use Caution Dear FreeSurfer experts, I am currently running longitudinal analyses using the paired analysis tutorial for two time points. There are two tests I am trying to run: 1. Calculating significant changes in volume between the two time points, controlling for age and gender. 2. Correlating BMI with change in volume between the two time points, controlling for age and gender. For (1), would it be necessary to demean age for a one-sample longitudinal analysis? And for (2), would I need to demean both BMI and age? Thank you for your help.

2 1

mri_convert help w/ GE Genesis files
by Christopher Mcnorgan 24 Jun '21

24 Jun '21

External Email - Use Caution Hi all, I’ve been provided with some data collected on a 1.5T GE scanner from an old published study. The paper doesn’t indicate the scanner model (beyond that it’s a 1.5 GE scanner), but I believe they came from a GE Genesis, based on the .MR file extension. I have successfully used MRIcro to convert the series of .MR files from the anatomical scan to Analyze format, so there’s nothing wrong with the files. I would prefer to script mri_convert to convert the data, but I am having problems doing so, as each of my attempts results in a segmentation fault. Files were originally named <pattern>1.MR to <pattern>128.MR, and based on the program output prior to the core dump, I renamed them so that the file numbers were zero-padded, and I’ve tried it with and without the input filetype argument, but I get the segmentation fault/core dump either way. The command I’m trying is: mri_convert -i E11816S5I001.MR -it ge -o T1.nii.gz This gives me: reading from E11816S5I001.MR... fname_format : /home/fruit/music/tmp/E11816/mri/S5/renumbered/E11816S5I%d.MR fname_format2 : /home/fruit/music/tmp/E11816/mri/S5/renumbered/E11816S5I%03d.MR Segmentation fault (core dumped) I was hoping someone could point out something that I’m missing. Thanks for your time. It’s much appreciated. /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://secure-web.cisco.com/11HrmGviCIYIvUr8zM_GIo6mtULm1BjCwyqj-E9atrNMCWU… * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/

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T2 T1 registration with mri_robust_register
by Marina Fernández 24 Jun '21

24 Jun '21

External Email - Use Caution Dear experts, I would like to co-register T2 to T1 robustly, both images have a resolution of 0.65mm3. Firstly, I tried bbregister with the '--init-rr' flag, but this function doesn't allow to keep the native voxel resolution (i.e., 0.65mm3), changing it to 1 mm. As I wanted to maintain the native voxel resolution , I tried the mri_robust_register function (corresponding to the '--init-rr' flag) as explained in the help associated with this function, but this process took thirteen hours: EXAMPLE 4. Robust cross modal registration: mri_robust_register --mov movT2.mgz --dst dstT1.mgz --satit --iscale --mapmov T2_to_T1.mgz --lta T2_to_T1.lta --cost ROBENT --entradius 2 --entcorrection --weights T2_to_T1_weights.mgz I also tried the standard cross modal registration. The process didn't take as long, but the result was not as accurate as bbregister. EXAMPLE 5. Standard cross modal registration: mri_robust_register --mov movT2.mgz --dst dstT1.mgz --mapmov T2_to_ T1.mgz --lta T2_to_T1.lta --cost NMI Could you suggest me how to accurately register T2 to T1 images maintaining the native voxel resolution in a shorter time? Thank you very much in advance. Best, Marina

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The specific steps of the mri_surf2surf command
by 1248742467 24 Jun '21

24 Jun '21

External Email - Use Caution Hello, Fs I am not familiar with the exact steps of sampling a pre-segment file into the FSAVERAGE5 space. In other words, I am not very familiar with the exact steps of the mri_surf2surf command.

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