Freesurfer January 2022

freesurfer@nmr.mgh.harvard.edu

69 participants
112 discussions

movement correction using 24 movement parameters or stick regressors to remove volumes
by stdp82＠virgilio.it 26 Jan '22

26 Jan '22

External Email - Use Caution Hi list, in functional connectivity assessment by FS-FAST, is possible to do movement correction using 24 movement parameters including derivatives or stick regressors to remove the volumes for which the FD value (framewise displacement) is superior to 0.5 mm (see Tapas procedures for physiological noise correction in Frassle et al., 2021 https://secure-web.cisco.com/19GvmE_VjebaugWB4X8sbjJje0pY5b_NU8J63aVJIrlpYM… Thanks Stefano

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Visualization of data
by Paul, Rahul 26 Jan '22

26 Jan '22

Hi FreeSurfer experts, I have a dataset of 60 patients. Is there a way to visualize the average cortical thickness/area for my dataset? Thank you in advance. Rahul

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dcmunpack multiple runs together
by Shi, Yuelin 26 Jan '22

26 Jan '22

External Email - Use Caution Hello FreeSurfer Developers, I am using dcmunpack to unpack a data session that is composed of many series/runs. It seems that I can only feed in unpacking rules for one of the runs at a time by the "-run run subdir format stemname" command. Also for each data session like this, it seems I'll need to manually type in the run number and its rule everytime. We actually just moved from a Siemens scanner to a GE scanner. With Siemens, the unpacksdcmdir function accept seqcfg file that only needs to be written once and will be able to apply to any sessions. I wonder with dcmunpack 1) if there is at least a command that allows unpacking all the runs together? 2) Moreover, is there a way to specify the whole set of rules as a seqcfg file that will be easily applied to all future sessions? Thank you very much! Best, Yuelin

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statistical analysis of the volume of the hypothalamus_seg
by Xiaotong Zhang 26 Jan '22

26 Jan '22

External Email - Use Caution In the statistical analysis of the volume of the hypothalamus_seg, since the skull size of each person is different, it is necessary to exclude the influence of head size, that is, to regress the total intracranial volume, such as e TIV or sb TIV. I have a question: because the hypothalamus is the smaller subcutaneous nucleus, which indicator is more suitable for the analysis of the hypothalamus subregion? In addition, if the total volume of the hypothalamus as regression, is feasible? 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-dev 2) Platform: CentOS 7.9 Sincerely, Zhang

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Error in mri_glmfit
by Laura Willers de Souza 26 Jan '22

26 Jan '22

External Email - Use Caution Hello FreeSurfer Developers, I want to perform an analysis of the difference between two groups in cortical thickness, having cortisol levels as covariate. This is my model: cortical thickness ~ diagnosis (CU/CI) + plasma cortisol + diagnosis*plasma cortisol I am now performing a glm dods analysis to see if the diagnosis*plasma cortisol interaction is significant. I'm using this contrast: 0 0 1 -1 The fsgd file is attached. Cortisol values are converted to log. But when I run the mri_glmfit command it gives the following error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------- ERROR: READ THIS ----------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y lh.CU_CI_plasma.thickness.10.mgh --fsgd CU_CI_plasma.fsgd dods --C group-x-cortisol_pl.mtx --surf fsaverage lh --cortex --glmdir lh.CU_CI_plasma.glmdir --eres-save 2. The terminal output of this program (ie, everything it prints to the screen) 3. The FSGD file (CU_CI_plasma.fsgd) - ATTACHED 4. The design matrix lh.CU_CI_plasma.glmdir/Xg.dat - ATTACHED Attempting to diagnose further SumSq: Min=0.000000 (col 3), Max=22.135944 (col 2) The scale is much different between columns 3 and 2, you may want to normalize by subtracting the mean and dividing by the standard deviation. Column 3, all values are 0 Column 4, all values are 0 Columns 3 and 4 are the same Could this error be because the n of the CU group is 54 and of the CI group is 490? Thanks in advance! Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

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Re: [Freesurfer] Spatial distance between regions
by Julie Ottoy 26 Jan '22

26 Jan '22

External Email - Use Caution Hi Doug, Just checking in with the question below. Does Freesurfer have such an option? Thanks, Julie On Tue, 14 Dec 2021 at 18:38, Julie Ottoy <julie.jj.ottoy(a)gmail.com> wrote: > Hello FreeSurfer team, > > I was wondering if there is a way to calculate a distance matrix between > atlas-based regions (e.g. between their centers of mass) in volumetric > space (MNI152) space? > > Thank you for the information! > Best regards > Julie >

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mri_info orientation string ???
by Xiaojiang Yang 26 Jan '22

26 Jan '22

External Email - Use Caution Dear Freesurfer Experts, I have a question regarding the orientation string gotten from mri_info. When I apply mri_info command to a DIOM series I generated programmatically, I get the "???" result, and hence primary slice direction is also unknown: ...... Orientation : ??? Primary Slice Direction: unknown ...... I already had the " Image Position Patient" and "Image Orientation Patient" written in the DICOM header. Don't know what other important info is missing. Could you tell me what key information is used in DICOM header to determine this orientation when using mri_info? Thanks! John

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opposite results between QDEC and SPSS
by baobao 26 Jan '22

26 Jan '22

External Email - Use Caution Hello, Freesurfer experts: I have encountered some problems when using QDEC analysis in Freesurfer 6.0. Because some picture need to be shown, so these problems was displayed in the attachment.Thank you for your kindness, and your prompt attention to this letter will be highly appreciated. Sincerely, Weijie Bao Postgraduate Huaxi MR Research Center(HMRRC) Department of Radiology West China Hospital of Sichuan University Chengdu, Sichuan, PR China, 610041 Tel: 86-13594527190 Email: 13594527190(a)163.com

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Question about fsaverage
by zhoudongyue＠mail.dlut.edu.cn 26 Jan '22

26 Jan '22

External Email - Use Caution Dear FreeSurfer experts: I am confused how vertex position is determined.  Is the vertex's position on surface is determined? And is the distance between each two vertex the same？ Bests， dongyue <html> <head> <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> </head> <body> </body> </html>

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mkheadsurf error: mris_smooth and mris_inflate synthesized bizarre output paths
by Yong-Jun Lin 26 Jan '22

26 Jan '22

External Email - Use Caution Hello FreeSurfer Developers, I was attempting to execute the mkheadsurf script to process MRI data and encountered some errors. 1. The first error message is "subjdir: Undefined variable.". After reading through the mkheadsurf script, I realized that is a temporary variable used in a script. Having no idea why this was required in the beginning, I manually entered export subjdir=/Volumes/Lab/SA/MRI/ForMNE/subj01 to circumvent that problem. 2. Indeed the script started running afterwards, but there were two errors at step 1. (Creating a dense scalp tessellation with mkheadsurf) First, mris_smooth -n 10 -b /Volumes/Lab/SA/MRI/ForMNE/subj01/surf/area.seghead -c \ /Volumes/Lab/SA/MRI/ForMNE/subj01/surf/curv.seghead \ /Volumes/Lab/SA/MRI/ForMNE/subj01/surf/lh.seghead \ /Volumes/Lab/SA/MRI/ForMNE/subj01/surf/lh.seghead resulted in error: MRISwriteCurvature: could not open lh./Volumes/Lab/SA/MRI/ForMNE/subj01/surf/lh.curv.seghead Second, mris_inflate -n 10 -sulc /Volumes/Lab/SA/MRI/ForMNE/subj01/surf/sulc.seghead \ /Volumes/Lab/SA/MRI/ForMNE/subj01/surf/lh.seghead \ /Volumes/Lab/SA/MRI/ForMNE/subj01/surf/lh.seghead.inflated resulted in error: MRISwriteCurvature: could not open /Volumes/Lab/SA/MRI/ForMNE/subj01/surf/lh./Volumes/Lab/SA/MRI/ForMNE/subj01/surf/lh.sulc.seghead Please note that the weird output paths have the output folder repeated twice in different positions. 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 the mkheadsurf.log in case it's of any use. 1) FreeSurfer version: freesurfer-darwin-macOS-7.2.0 2) Platform: macOSX 10.13.6 3) uname -a: Darwin localhost 17.7.0 Darwin Kernel Version 17.7.0: Fri Oct 30 13:34:27 PDT 2020; root:xnu-4570.71.82.8~1/RELEASE_X86_64 x86_64 4) mkheadsurf.log: see attached Sincerely, -- Yong-Jun Lin Postdoctoral Associate Department of Psychology New York University 6 Washington Place, Room 955 New York, NY 10003

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Freesurfer January 2022