Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30085 discussions

Infant FreeSurfer
by k3ops＠free.fr 29 Sep '20

29 Sep '20

External Email - Use Caution Hi FreeSurfer team, I’ve been using the Infant FreeSurfer pipeline on 3DT1 sequences for few weeks now on infants from 0.4 to 5.4 years-old. I know Infant FreeSurfer is recommended for 0-2 years old infant but standard FreeSurfer was failing due to many lacunar infarcts in the white matter. So I tried Infant FreeSurfer with an age of 2 years old even for 2 to 5.4 years-old subjects and results look good. I know standard FreeSurfer has been tested on infant from 4.2 years-old, so what would be your recommendation for subjects from 2 to 4.2 years old? Have you already run Infant FreeSurfer on subjects older than 2 years-old? Do you recommend it? I also have some processing issues (see below) with my actual data: 1. Pixels with 0 value => probably out of the brainmask so the pixels are set to 0 after masking So, sometimes lateral ventricles are miss-segmented (see "pixel_0_brainmask" attachment) 2. Thalamus region is missing from the aseg stat export (always equal to 0 mm3), do you have a fix? Should I fix a LUT file? 3. Would it be possible to get the non-skullstripped N3 corrected 3D T1 in the MNI space (3D iso)? I was not able to find the registered 3DT1 to re-apply the N3 correction, I only found the input 3DT1 (mprage.nii.gz) in its native space. 4. Do you have any workaround for large ventricles segmentation issue (see "large_ventricles" attachment)? Standard FreeSurfer has a -bigventricle option, do you have a similar approach? And some additional questions: • brainstem seems to be split into multiple sub-regions, is it possible get the entire brainstem volume in the aseg stat export? • I saw that corpus callosum is not present in the “aseg” segmentation, so is this region out of the Infant FreeSurfer atlases? • Is it possible to get the mean cortical thickness for the labels you are providing? Many thanks as I know there are plenty of questions here :) Best, Florent

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Re: [Freesurfer] vol2surf: lesion overlap across group into surfaces
by Douglas N. Greve 28 Sep '20

28 Sep '20

The question is more for you. The lesions are not on the surface but you want to display them on the surface. How do you want to do that? ps. please remember to post to the list On 9/10/2020 10:25 AM, Horn, Mitchell Jacob wrote: > > Thanks so much Douglas. > > Many of the lesions are in the white matter, and many span across WM > and GM. In the case where the lesions on not strictly cortical, is > this surface mapping not possible? Or perhaps a representative surface > map showing the occurrences of lesions in any lobe/ROI? > > Best, > > Mitch >

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Errors running TRACULA (data attached)
by ksak666＠yahoo.co.jp 28 Sep '20

28 Sep '20

External Email - Use Caution Dear FreeSurfer Developers, I'm attempting to run Tracula using our subjects DTI nifti files on Freesurfer version 7.1.1 (Ubuntu 18.04). I could run all steps of "trac-all" commands in a single subject using the attached configuration file (dmrirc_MULhos554s). However, I failed to analyze subjects group using the attached another configuration file (dmrirc_edit). After "trac-all -prep -c dmrirc_edit" command, I always got a same error message written below. sakurai@ubuntu:~/Desktop/freesurfer/tracall$ trac-all -prep -c dmrirc_edit ERROR: must specify as many fieldmap magnitude dicoms as subjects I have checked the mail archives and tried to troubleshoot.But I could not find an adequate solution because of a shortage of knowledges to make appropriate configuration files. Please tell me how to make an appropriate configuration file. Best regards, Keita SakuraiDepartment of RadiologyNational Center for Geriatrics and Gerontology ****************************************Keita Sakurai E-mail: ksak666(a)yahoo.co.jpDepartment of RadiologyNational Center for Geriatrics and Gerontology7-430 Morioka-cho, Obu, 474-8511, Aichi, Japan

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mri_extract issue
by Jie Zhao 27 Sep '20

27 Sep '20

External Email - Use Caution Hi, Freesurfer Team My input volume dimension is 248*176*320, so I use mri_extract scale to 256*256*256. However, the output volume lose some info. eg.some head info. disappeared in sagiital slice. How can scale my input voluem to 256*256*256, and also do not lose info.Thanks in advance! All best, Jie

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Maximum N of inputs in fsgd file
by Cordova Palomera, Aldo 25 Sep '20

25 Sep '20

External Email - Use Caution Dear FreeSurfer experts, When running mri_glmfit, there seems to be an upper limit of 20000 inputs on an fsgd file, as suggested by the error message below: ERROR: gdfReadV1: the number of inputs in FSGD file exceeds the maximum allowed 20000 By any chance, is there a way to expand this limit, or is there an alternative version of mri_glmfit to avoid this? Here's the FS version that showed the error above: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Thanks, The content of this email and of any files transmitted may contain confidential, proprietary or legally privileged information and is intended solely for the use of the person/s or entity/ies to whom it is addressed. If you have received this email in error you have no permission whatsoever to use, copy, disclose or forward all or any of its contents. Please immediately notify the sender and thereafter delete this email and any attachments.

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Re: [Freesurfer] parameterization template and the vertex in the pial surface
by Pam Garcia 25 Sep '20

25 Sep '20

External Email - Use Caution Thanks for your response Bruce, just to clarify If I understood, the wm surface is created using a surface deformation procedure that adaptively determined the MR intensity of the boundaries in question at each point in the cortex. Next a sphere from the wm inflated surface is computed, warps the sphere into a 2-D file containing the curvature and convexity patterns of the subject, and then registers the 2D file with a reference (parameterization template). This is executed to ensure that the curvature and convexity patterns are aligned with a generic reference template. The mean and the variance of curvature and convexity from the smooth and inflated surface are used in order to do more robust the register. Finally, the pial surface is created by expanding the white matter surface so that it closely follows the gray-CSF intensity gradient, keeping the same topology (number of vertex, edges, faces) and the vertex index is preserved. Finally, the vertex of the wm and pial surface are mapped in a common space and is here where we obtained vertex correspondence across the subjects. Thanks

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error generating pial surface after skullstrip and gcut
by KennethSPrice 25 Sep '20

25 Sep '20

External Email - Use Caution Hello, I ran recon-all -skullstrip -gcut and am trying to generate the pial surfaces again. I get an error: Reading in intensity volume brain.finalsurfs.mgz Reading in wm volume wm.mgz Reading in surf ../surf/lh.orig.premesh error: No such file or directory error: MRISread(../surf/lh.orig.premesh): could not open file Command exited with non-zero status 1 Could you please explain what is wrong and how to fix? Thanks, Ken Sent with [ProtonMail](https://protonmail.com) Secure Email.

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Error when running aparcstats2table: list index out of range
by Hye Min Shin 25 Sep '20

25 Sep '20

External Email - Use Caution Hello experts, I am having trouble running aparcstats2table on a group of subjects. Everytime I run aparcstats2table I get this error: python2 $FREESURFER_HOME/bin/aparcstats2table --hemi lh --subjectsfile=$(pwd)/final_list.txt -t $(pwd)/lh.test.dat --parc aparc.mapped --delimiter comma --meas thickness Parsing the .stats files Traceback (most recent call last): File "/usr/local/freesurfer/bin/aparcstats2table", line 376, in <module> parc_measure_map = parsed.parse(options.meas) File "/usr/local/freesurfer/bin/fsutils.py", line 215, in parse val = float(strlist[self.measure_column_map[measure]]) IndexError: list index out of range My current freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Now I did set my SUBJECTS_DIR to the folder with subjects files. And I was able to successfully run aparcstats2table previously with other subjects. When I ran aparcstats2table separately for a couple of subjects, it did run successfully. I thought there must be some carriage return with the text file of the list of subjects so I made sure to remove any carriage returns. Best, Julia Shin

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Masking surface overlays and spatial correlations
by Mason Wells 25 Sep '20

25 Sep '20

External Email - Use Caution Hi Experts, I wonder if anyone can give me any advice on a couple of things. 1) I have some ICA spatial maps which I have resampled to the surface using bbregister and vol2surf. I can load this data in Freeview as a generic overlay (see attched). I also have a label file which is a combination of several visual areas. What I want to do is use this label as a mask and remove any activation from the ICA map overlay which falls outside of the label/mask. Is this possible using Freesurfer? In FSL I have been using fslmaths with -mas flag. 2) My next question is whether it is possible to run spatial correlations on the surface. For example, I would like to know how well my ICA component maps match with some visual areas labels I have created in Freesurfer. In FSL i have been using fslcc to run these correlations between my ROIs and the spatial maps in the volume. Thanks in advance, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-><http://www.cardiff.ac.uk/people/research-students/view/482937-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628

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Freesurfer vs 6 Cortical Surfaces and vs 7.1.1 Subcortical areas
by Annelies Vant Westeinde 25 Sep '20

25 Sep '20

External Email - Use Caution Hello list, I noticed that I find the quality of the neocortical segmentation of vs 6 better than vs 7.1.1., but the subcortical segmentation of 7.1.1 better than vs 6. Is it valid to do analyses of neocortical and subcortical areas based on different Freesurfer versions? Even when, say, correlating them to each other? Or, in line with this to use the hippocampal and amygdala subfields from vs 7.1.1 in combination with neocortex (eg thickness estimates) of vs 6? Thank you! Annelies Annelies van't Westeinde | PHD Candidate Department of Women's and Children's Health | Karolinska Institutet 171 77 Solna | Karolinskavägen 37A +46 760967499 annelies.vant.westeinde(a)ki.se | ki.se<http://ki.se/en/startpage> ______________________________________ Karolinska Institutet – a medical university När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>.

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