Freesurfer May 2022

freesurfer@nmr.mgh.harvard.edu

86 participants
124 discussions

Unit of the Numbers in cache.th40.neg.y.ocn.dat
by Na, Xiaoxu 17 Feb '24

17 Feb '24

External Email - Use Caution Dear Freesurfer Experts, As I'd like to extract the average value of each subject in the cluster after running group analysis, may I know the unit of these numbers? Since the one I'm running is surface area, and the cluster is 444mm^2, all the numbers in the file cache.th40.neg.y.ocn.dat is in the range of [0.55 1.05], may I know if this is correct and if so, how the unit is for those? Thanks a lot! ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx 1 -4.8321 40067 444.11 -58.1 -16.6 -23.9 0.0002 0 0.0004 670 -2784.11 Regards, Xiaoxu ---------------------------------------------------------------------- Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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Extract single time frame
by Rockers, Elijah D. 16 Oct '22

16 Oct '22

Hello again, I have a large time series in dicom or .nii format. I am interested in extracting a single time frame from it. I did this before, I believe with freesurfer, but I have somehow forgot the name of the command, and I can't seem to find it. I believe it could be used to specify particular regions of the volume, as well as time. I need the entire volume, still, but only one frame. Thanks in advance! Eli Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list 10 years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Reliability and sensitivity of two whole-brain segmentation approaches − ASEG and SAMSEG
by Donatas Sederevicius 28 Aug '22

28 Aug '22

External Email - Use Caution A new pre-print paper comparing two FreeSurfer’s whole-brain segmentation methods - ASEG and SAMSEG is now available (see the link below). The study is of great interest to many researchers in the field, providing new insights and guiding the selection of the processing method. https://www.biorxiv.org/content/10.1101/2020.10.13.335737v1

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SAMSEG and statistics
by k3ops＠free.fr 27 Aug '22

27 Aug '22

External Email - Use Caution Hi FreeSurfer community, I recently discovered the SAMSEG application in the FreeSurfer 7.2.0 release and started to give a try on few subjects were FreeSurfer was having a hard time to segment brain structures (due to poor contrast). So I have few questions to harmonize the SAMSEG and FreeSurfer statistical files: 1. "samseg.stats" file is not compliant with the "asegstats2table" application so I was not able to generate a final CSV file with volumetric results Is there another solution? 2. "samseg.stats" file does not provide large brain structures like "BrainSegNotVent" or "SupraTentorialNotVent", is there a way to get them calculated? 3. "samseg.stats" file does not provide left/right or global cortical thickness, is there a command line to execute to get these extra values? Thanks. Best, Florent

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Recon All
by Amar Shukla 21 Jul '22

21 Jul '22

External Email - Use Caution Dear Sir, I am a PhD scholar using the freesurfer tool to conduct my research work. I tested the recon all method in the Free Surfer, and it was effective with the data set that was used by me. What are the exact default parameters for the different processes of recon all that were used in motion correction, intensity normalization, etc?. It would be really helpful if you could provide me with the link or the article where it is explained clearly, this will help me to get through these processes in more depth and in a more constructive manner. Although the Free Surfer website has an FAQ regarding this process, there are no clear explanations about what the default parameters are during recon all. -- With Regards, Amar Shukla PHD Scholar UPES

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HRF with derivatives: results
by Laura Doll 09 Jun '22

09 Jun '22

External Email - Use Caution Hi everyone, I need some help regarding the SPM-HRF with two derivatives: Where can I find the actual function that was used for the analysis? I am mostly interested in the peak latency, but would also appreciate if I can check the other parameters of the function somewhere. Best, Laura

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creating. or replacing a label of choice in aseg atlas
by Ramtilak Gattu 09 Jun '22

09 Jun '22

External Email - Use Caution Hi, We are interested in replacing a couple of labels in aseg atlas with our own roi's already in the same space as of "aseg.mgz" atlas in the fsaverage folder. What would be the best way to do this? Could someone help or guide me if anyone has done something similar to this query? Can I just add the regions (in the form of 3d masks) to the aseg atlas and create aseg_modified.mgz and later replace the aseg.mgz with aseg_modified.gz and rename the aseg_modified.mgz back to aseg.mgz. If I follow this procedure and run "recon-all" will the aseg_stats will give me volumes based on the new volumes? -- Regards Tilak

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aseg and surface edit corrections - grey matter surface fails editing
by Helena Pereira 07 Jun '22

07 Jun '22

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to get the new surface pial from the grey-matter. I note that the grey-matter from the temporal areas is not correctly segmented (a few slices are not identified as grey-matter nor with any label) in the aseg file, which influences the surface pial of the grey matter. To correct this, I manually corrected the aseg file expecting to get the correct surface pials. Nevertheless, after running recon-all make -all, the surface remains the same. I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, I've attached an example of my problem, after recon-all make -all. 1) FreeSurfer version: 7.1.1 2) Operating system info: AlmaLinux 8.5, rhel centos fedora 8.5 Thanks in advance, Best regards, Helena Pereira

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samseg2recon error / missing files
by Jacob Levenstein 01 Jun '22

01 Jun '22

External Email - Use Caution Hello Freesurfer team + users, I am looking to run segmentHA_T1.sh following samseg + samseg2recon, and came across this previous thread where it seemed to workout: https://secure-web.cisco.com/1u2xTmmnCUaxQQuSTDRURAlZzdIaStC1AkxmbcmeQ18lFv… Given that I am writing in, I have not yet gotten this to run properly... Below is my samseg command: samseg --t1w ${subject}_${ses}_T1w.nii.gz --sd . --s ${subject}_${ses}_samseg --refmode t1w --threads 16 --parallel >From the log file, samseg seems to run correctly, but once it reaches the samseg2recon steps, I receive the following error: ln -sf orig.mgz rawavg.mgz ERROR: ln -sf orig.mgz rawavg.mgz ERROR: samseg2recon --s ${subject}_${ses}_samseg --tmpdir ${SUBJECTS_DIR}/${subject}_${ses}_samseg/mri/samseg/tmp.pyBLVF/tmp.mergeseg --cleanup If I then (re)run samseg2recon on the samseg directory (see cmd below) , I can execute the failed lines, and this script completes without error. samseg2recon --s ${subject}_${ses}_samseg However, when I then try to run: segmentHA_T1.sh ${subject}_${ses}_samseg, I receive the following error: Cannot find wmparc.mgz or norm.mgz or talairach.xfm for the subject. Has the subject been procesed with recon-all? As the error message correctly states, within that subject's dir, I do not have an mri/norm.mgz or mri/wmparc.mgz. I do have an mri/samseg/transforms/samseg.talairach.xfm, but it is not in the scripts expected location/naming convention. If it is helpful to know: i. Running recon-all then segmentHA_T1.sh completes without error... ii. Copy over the mri dir from the recon-all to the samseg subject dir, then running segmentHA_T1.sh also completes without error... iii. I am running Ubuntu 20.04.4, freesurfer-linux-ubunu18x86_64_-7.2.0-20210721 Any idea what may be going wrong with samseg/samseg2recon? I am happy to use the workaround listed above, but I suspect there may be a more efficient way, and or unintended implications when mixing and matching recon-all and samseg...? Thank you for your help and insight! All the best, Jacob

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fmcpr.up.sm5.mni305.2mm.nii.gz label
by Mingyang Xia 01 Jun '22

01 Jun '22

External Email - Use Caution Dear Freesurfer expert: I am Mingyang Xia. I use freesurfer to preprocess the fmri data and map to the fsaverage and generate a file named fmcpr.up.sm5.mni305.2mm.nii.gz. I want to get the label of this file however I could not find the label in the fsaverage folder. Could you give me some advice? Thank you Mingyang Xia

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Freesurfer May 2022