Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30131 discussions

Postdoctoral position
by neuroimage analyst 20 Mar '21

20 Mar '21

External Email - Use Caution Hi. We are looking for a postdoc to work with us on multimodal MRI and machine learning to predict Parkinson's disease dementia. An ideal candidate should be well versed and understand multi-shell diffusion MRI analysis and processing and have an interest in developing models for fusing across different MRI and non MRI modalities via deep learning or machine learning models. Contact me directly for more information or Apply here https://secure-web.cisco.com/1esZWcZk9kteVZxe-rcxz8vEdu1K9larHO-dBsWZn3e4QK… Apologies for cross posting. Thank you.

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equivolumetric surfaces
by バキット・ムダシル 20 Mar '21

20 Mar '21

External Email - Use Caution Dear freesurfer experts, I want to create an equivolumetric surfaces (using the tool from: https://secure-web.cisco.com/1RxQBNBh7QLlgBP46WWIONAGLCrtuooPBalXpNMTOlsF1e… <https://secure-web.cisco.com/1RxQBNBh7QLlgBP46WWIONAGLCrtuooPBalXpNMTOlsF1e…>) and to sample the intensities of the T1wDividedByT2w volume at all the depths. I created the surfaces and after running the mri_vol2surf command I faced the error below. I don’t know why the path to the surface is not correct. I tried it in different devices with different versions of freesurfer but the results were the same. Any idea what I did wrong? Thanks Mudathir ################################################# -------- freesurfer-darwin-macOS-7.1.1-20200811-8b40551 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer/7.1.1 FSFAST_HOME /Applications/freesurfer/7.1.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/7.1.1/subjects MNI_DIR /Applications/freesurfer/7.1.1/mni FSL_DIR /usr/local/fsl mudathir% mri_vol2surf --src $SUBJECTS_DIR/spl_01/mri/T1wDividedByT2w.nii.gz --out $SUBJECTS_DIR/spl_01/lh.equi_intensity_1.0.mgh --hemi lh --surf $SUBJECTS_DIR/spl_01/surf/lh.equi1.0.pial --out_type mgh --regheader spl_01 srcvol = /Applications/freesurfer/7.1.1/subjects/spl_01/mri/T1wDividedByT2w.nii.gz srcreg unspecified srcregold = 0 srcwarp unspecified surf = /Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /Applications/freesurfer/7.1.1/subjects/spl_01/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.35001; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Reading surface /Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial error: No such file or directory error: MRISread(/Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial): could not open file error: No such file or directory error: mri_vol2surf: could not read surface /Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial mudathirbakhit% #################################################

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mri_extract_label mgz to nii ， maximum grayvalue of amygdala subnucleis is zero.
by 况况 19 Mar '21

19 Mar '21

External Email - Use Caution TO: freesurfer(a)nmr.mgh.harvard.edu SUBJECT: mri_segstats error: mri_extract_label mgz to nii Hello FreeSurfer Developers, I'm want to study the volume and function of amygdala subnucleis, so i need to acquire the mask of amygdala subnucleis in MNI space. mri_extract_label subject_001/mri/lh.hippoAmygLabels-T1.v21.mgz 7001 lateral_nucleus_001.nii i total 77 subjects,including left and right amygdala subnucleis , totally acquired 77*18=1332 nii files. Reading the maximum grayvalue of 1332 nii files , and 5 nii files maximum grayvalue is zero. |'lh.Anterior-amygdaloid-area-126.nii'| |'lh.Medial-nucleus-111.nii'| |'lh.Medial-nucleus-319.nii'| |'rh.Anterior-amygdaloid-area-417.nii'| |'rh.Anterior-amygdaloid-area-428.nii'| I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0 2) Platform: CentOS release 6

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Error flag i <file path> unrecognized
by Timothy Brackins 19 Mar '21

19 Mar '21

External Email - Use Caution Hello FreeSurfer Developers, I am brand new to using freesurfer, just learning for the first time. I have freesurfer installed and sourced on linux Ubuntu 18.04.5 LTS. My NfTI files are stored on a windows share drive which I mount to the linux machine. Upon entering the recon-all command I receive the Error flag i <file path> unrecognized. I searched the archives but did not see a similar issue.Thank you in advance for your time and help with this. -- Timothy Brackins Doctoral Student, Cognitive Sciences Cognitive Aging and Memory (CAM) Lab Stony Brook University Email: timothy.brackins(a)stonybrook.edu <julia.kearle(a)stonybrook.edu> Lab Website: https://secure-web.cisco.com/1Ry_JC145aM8XwIFAq-LQSD7fYGd_v5PVnOcPMnS80qPgG…

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Prevent segmentHA_T1_long.sh from creating several LWPs
by Micael Andersson UMU 19 Mar '21

19 Mar '21

External Email - Use Caution Dear FreeSurfer users I have been running the longitudinal pipeline with hippocampus segmentation in FreeSurfer 7.1.1 on a computer cluster with a batch-system that regulates number of cores to use. There is though a problem when running /segmentHA_T1.sh/ and /segmentHA_T1_long.sh/ since they creates several LWPs. Setting /export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1/ does lock a process to one core at a time, but NLWP is not 1, which is a problem on the cluster system. Does anyone know how to solve this problem? Best regards Micael -- Micael Andersson Forskningsingenjör / Research engineer Umeå centre for Functional Brain Imaging (UFBI), http://secure-web.cisco.com/1FVOAhfwsPjDydJp65dw8Jr7D6RjBpT0ekDZTL4Olv87Usm… IMB, http://secure-web.cisco.com/1b9zLIOnP6D3n8IxdAvOLEP45ia7eb0r2jLKePKBOD0wuU7… Umeå universitet / University of Umeå När du skickar e-post till Umeå universitet innebär det att universitetet behandlar dina personuppgifter. Läs mer här: http://secure-web.cisco.com/127kZD8iFGMg4-p6Kat01Bm5EnfhpuTO0YX-PZEricNYuxx… By sending an email to Umeå University, the University will need to process your personal data. For more information, please read: http://secure-web.cisco.com/1Navs0amoVnm_DMw_6OVnHiV5Dl_vreYGzeu71n23GmQT5a…

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Cortical thickness on version 6 vs 7
by Xiaojiang Yang 18 Mar '21

18 Mar '21

External Email - Use Caution Dear Freesurfer developers, I have a cohort of subjects that are already run under FS 6. I recently upgraded Freesurfer from 6.0 to 7.1.1, and now I also have run these subjects under FS 7. When comparing the cortical thickness results obtained from FS6 and FS7, I found that FS 7 results are much smaller than the FS6 ones. On average, about 13%-21% decrease in the subject's average cortical thickness. Specifically, on a cohort of images from GE scanners, the average cortical thickness from FS6 is 2.5mm, but from FS7 is less than 2.0mm. According to some published papers, I think 2.5mm as the average cortical thickness is more accurate than 2.0mm. Have you encountered this issue or question before? Do you think I should keep using FS6? Please give me your advice. Thank you! John.

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Samseg longitudinal processing
by Jayachandra Raghava 18 Mar '21

18 Mar '21

External Email - Use Caution Hello Freesurfer Experts, I am using Freesurfer version 7.1.1 to perform longitudinal Samseg processing (using run_samseg_long) on my T1 longitudinal data. 1) First, I run the mri_robust_template to generate the mean.mgz using T1.mgz from the cross sectional recon-all pipeline. Would it be better to use T1.mgz from the longitudinally processed data? 2) There are few subjects who do not have followup data. How do I process these subjects to avoid the bias introduced by the longitudinal Samseg pipeline? 3) For the same subject, I see that the subcortical volumes from longitudinal recon-all pipeline from aseg.stats (e.g Left-Hippocampus volume is 3321.5mm3) are different to the subcortical volumes from longitudinal samseg pipeline from samseg.stats (e.g Left-Hippocampus volume is 3899.628686mm3). Which of these measures would be recommended? Thank you very much for your support! Best wishes Jay

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Putamen and claustrum
by Donatas Sederevicius 18 Mar '21

18 Mar '21

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: […] Putamen should be smaller because we now try to remove claustrum." Could you give a brief description of how you try to achieve it (if it is still the case)? Thank you. -Donatas

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7.1.1 recon-all steps verification
by Jaiashre Sridhar 18 Mar '21

18 Mar '21

External Email - Use Caution Hello, I am using FreeSurfer version v7.1.1. For few subjects who have already been through the complete recon-all pipeline, I would like to re-run the recon steps downstream of “-fill”. I am using the following commands to do so. Can an expert check and let me know if this encompasses all the downstream steps accurately for v7.1.1? ### Recon commands begin ### recon-all -s [subjid] -tessellate -smooth1 -inflate1 -qsphere -fix cd [subdir]/mri #-------------------------------------------- #@# AutoDetGWStats lh mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh #-------------------------------------------- #@# AutoDetGWStats rh mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh #-------------------------------------------- #@# WhitePreAparc lh mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 #-------------------------------------------- #@# WhitePreAparc rh mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 #-------------------------------------------- #@# CortexLabel lh mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 0 ../label/lh.cortex.label #-------------------------------------------- #@# CortexLabel+HipAmyg lh mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 1 ../label/lh.cortex+hipamyg.label #-------------------------------------------- #@# CortexLabel rh mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 0 ../label/rh.cortex.label #-------------------------------------------- #@# CortexLabel+HipAmyg rh mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 1 ../label/rh.cortex+hipamyg.label recon-all -s [subjid] -smooth2 -inflate2 -curvHK -autorecon3 ### Recon commands end ### Additional question – Is there an individual flag that replaces the hardcoded commands above for AutoDetGWStats, CortexLabel, WhitePreAparc and CortexLabel+HipAmyg? According to the [subjid]/scripts/recon-all.cmd file, I see that these additional commands are added to v7.1.1 but are not present in the recon steps listed here for stable 7.1.1 release https://secure-web.cisco.com/1mh5NrCnQZwjol6BqUWZ3zVU1wUDX0ceM5QaWcfAsgmEUH…. Thank you in advance for your response. Sincerely, Jaiashre.

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FreeSurfer brainmask.mgz: B-1 corrected?
by Arman Avesta 18 Mar '21

18 Mar '21

External Email - Use Caution Hi FreeSurfer gang, I'm using ADNI's pre-processed data to train a neural network. Specifically, for each included subject I'm using FreeSurfer Cross-Sectional brainmask.mgz (as input). My question is: are these ADNI pre-processed brainmask.mgz volumes already B1-corrected? (All ADNI subjects that I'm including in my project have B1 acquisition). If not, is there a simple way to perform B1 correction on brainmask.mgz? Thank you so much,Arman Arman Avesta, MD Radiology Resident & PhD Student Yale School of Medicine & Yale Graduate School of Arts and Sciences Email: arman.avesta(a)yale.edu Phone: 617-763-6632

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