Freesurfer

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30076 discussions

How to combine and divide surface-based fMRI data?
by Zhi Li 07 Nov '18

07 Nov '18

External Email - Use Caution Hello FreeSurfer experts, May I ask how can I modify the surface-based fMRI data, such as combing two independent sessions into one or dividing one 4D into a series of 3D surface-based fMRI files in which each one denotes a single volume/TR? Thank you very much. Best wishes, Zhi

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MatrixReadTxT: could not scan value [1][1]
by Anwar Shatil 07 Nov '18

07 Nov '18

External Email - Use Caution Hello Doug: My dti_recon is getting stuck at the "Fitting Tensor" stage. I was wondering if there is any solution to the problem "MatrixReadTxT: could not scan value [1][1]". My log file is attached here and the problem can be found right at the bottom. Is this a bug? What is the solution? There were similar reports on this earlier but nobody answered. https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subj… I am using FS 6.0 in MacOS. Best, Anwar

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Re: [Freesurfer] GLM
by Greve, Douglas N.,Ph.D. 07 Nov '18

07 Nov '18

Sounds like you need an F-test, eg, create a contrast like 1 1 -1 -1 0 0 0 0 0 0 0 0 1 1 0 0 -1 -1 0 0 0 0 0 0 This tests the null hypothesis that p1==p2==control On 11/07/2018 10:11 AM, 13181786167 wrote: > > External Email - Use Caution > > Thanks for your reply. Using the first one, We can obtain the sig.mgh > among 3 groups. If I want to obtain the results simultaneously between > patient 1 and 2, patient 1 and control, patient 2 and control. What > should I do. > > Sincerely, > Zheng > > > > > 郑凤莲 > 邮箱：13181786167(a)163.com > > <https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?iconUrl=h…> > > > 签名由网易邮箱大师 <https://mail.163.com/dashi/dlpro.html?from=mail88> > 定制 > > On 11/07/2018 22:57, Greve, Douglas N.,Ph.D. > <mailto:DGREVE@mgh.harvard.edu> wrote: > Use the first one. Not sure what you mean by your multiple > comparisons > question > > On 11/01/2018 11:20 PM, 郑凤莲 wrote: > > > > External Email - Use Caution > > > > Hi experts, > > > > I am using FS 6.0 for analyzing the cortical thickness > difference > > between 3 groups: patient1, patient2 and control. In DODS > model, I > > need to creat 2 files, FSDG and mtx file. And we have > 3 variables: > > age, gender and cortical thickness. > > 1. The FSDG file is: > > GroupDescriptorFile 1 > > Title Tutorial > > Class patient1-male > > Class patient1-female > > Class patient2-male > > Class patient2-female > > Class control-male > > Class control-female > > Variables age > > Input subject1 patient1-female 20 > > Input subject2 patient1-male 33 > > Input subject3 patient2-female 40 > > Input subject4 patient2-male 50 > > Input subject5 control-male 30 > > Input subject6 control-female 35 > > And there is another way: > > GroupDescriptorFile 1 > > Title Tutorial > > Class patient1 > > Class patient2 > > Class control > > Variables sex age > > Input subject1 patient1 1 20 > > Input subject2 patient1 2 33 > > Input subject3 patient2 1 40 > > Input subject4 patient2 2 50 > > Input subject5 control 2 30 > > Input subject6 control 1 35 > > What I want to confirm is that if I want to adjust for sex > and age, > > which one is right? > > Another question is that is there any way to get the multiple > > comparisons between groups simultaneously? > > I am looking forward to your reply. Thanks very much. > > > > Sincerely, > > Zheng > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Mapping a custom measure to the pial surface of fsaverage
by ts+ml＠rcmd.org 07 Nov '18

07 Nov '18

External Email - Use Caution Dear FreeSurfer experts, I have created a custom measure on the pial surface of a number of subjects, and I would like to map the data to the fsaverage subject. (By custom measure I mean something like 'area' or 'curv', i.e., one scalar value per surface vertex.) I have already done the same for the white surfaces, and it was pretty straight-forward: 1) Save the per-vertex data in a curv-format file in SUBJECTS_DIR/<subject>/surf/?h.<measure> 2) Run 'recon-all -s <subject> -qcache -measure <measure>' This will map the data to fsaverage and create files named ?h.<measure>.fwhm<n>.fsaverage.mgh in the surf/ directories as expected (where <n> is 0, 5, .., 25). My question is: how can I do the same for my data from the pial surface? Are there any command line options for 'recon-all' (or maybe for mris_preproc) that can do this? I already tried to put the pial per-vertex data into files named SUBJECTS_DIR/<subject>/surf/?h.pial.<measure>, but they are not handled by the recon-all command listed above: no fsaverage files show up for them. Thanks in advance, Tim -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

2 4

Extracting values from a single vertex
by Nillo, Ryan Michael R 07 Nov '18

07 Nov '18

External Email - Use Caution Hi FreeSurfer users, I want to extract thickness values at a single vertex. I searched on the support list and found an mris_convert command to use. However, the file I want to extract values from is a volume with multiple frames. When I try to use mris_convert on it, I only got the value at a vertex on the first frame. The goal is to set that vertex as a seed point and use the values as a regressor for glm. Is there a way to do this with FreeSurfer's commandline tools, or should I do this in Matlab? Mahalo, Ryan M Nillo Staff Research Associate I UCSF Department of Radiology and Biomedical Imaging

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applying the same edits to multiple scans
by Hanford, Lindsay C 07 Nov '18

07 Nov '18

Hello Freesurfer Experts, I am wondering whether it is possible to apply the same manual edits (removing GM/WM or adding CPs) to multiple scans. I have a dataset with ~100 scans per subject acquired in quick succession and, interestingly, Freesurfer appears to have the same issue in almost all of the scans (I guess that speaks to the reliability!). In this case, a small region of the optic nerve is being included as GM (and occasionally WM) so I am wondering whether I can reduce my time with manual edits by either (1) applying the same edits to multiple images, or (2) in this case, applying a more constrained mask to remove the possibility of including optic nerve within the brainmask. Thank you in advance, Lindsay

1 0

GLM
by 郑凤莲 07 Nov '18

07 Nov '18

External Email - Use Caution Hi experts, I am using FS 6.0 for analyzing the cortical thickness difference between 3 groups: patient1, patient2 and control. In DODS model, I need to creat 2 files, FSDG and mtx file. And we have 3 variables: age, gender and cortical thickness. 1. The FSDG file is: GroupDescriptorFile 1 Title Tutorial Class patient1-male Class patient1-female Class patient2-male Class patient2-female Class control-male Class control-female Variables age Input subject1 patient1-female 20 Input subject2 patient1-male 33 Input subject3 patient2-female 40 Input subject4 patient2-male 50 Input subject5 control-male 30 Input subject6 control-female 35 And there is another way: GroupDescriptorFile 1 Title Tutorial Class patient1 Class patient2 Class control Variables sex age Input subject1 patient1 1 20 Input subject2 patient1 2 33 Input subject3 patient2 1 40 Input subject4 patient2 2 50 Input subject5 control 2 30 Input subject6 control 1 35 What I want to confirm is that if I want to adjust for sex and age, which one is right? Another question is that is there any way to get the multiple comparisons between groups simultaneously? I am looking forward to your reply. Thanks very much. Sincerely, Zheng

2 1

aparcstats2table --parcs-from-file trouble
by Figueiro Longo, Maria Gabriela 07 Nov '18

07 Nov '18

Hi, I extracted some volumes using mri_annotation2lable --> mri_aparc2aseg --> mri_segstats <file>. Now I am trying to extract the summary table using aparcstats2table --parcs-from-file <file>, but every time an error message pops up: ERROR: cannot read <file> The stats files generated by the mri_segstats look correct (similar with the other files in the directory) and I can read the volumes of each individual. The last command that has an error is: aparcstats2table --qdec-long qdec.txt --hemi lh --meas volume --parcs-from-file <file> --tablefile volumes.txt I really appreciate any help! Thanks! Gabriela

2 1

First level modelling in task-based fMRI data
by Zhi Li 07 Nov '18

07 Nov '18

External Email - Use Caution Hi FreeSurfer Experts, Now I am trying FS-FAST in analyzing task-based fMRI data. We have two runs for each participant. However, there were not enough events in some runs of some participants. Hence we'd like to concatenate the preprocessed images of two runs into one rather than model them separately. How can we combine the preprocessed surface and sub-cortical data of each run into one? In addition. can we use FreeSurfer or FS-FAST to analyse task-based functional connections, such as psychophysiological interactions analysis and dynamic causal modelling? Do you have any suggestions? Thank you and best wishes, Zhi

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Re: [Freesurfer] Myelinated cortical thickness ratio map
by Damien MARIE 07 Nov '18

07 Nov '18

External Email - Use Caution Hi Matt, Many thanks for your prompt reply, you are right. Any tips on how I could do that? Should I regress out cortical thickness from my myelin maps at the individual level, save the individual output myelin maps and run analyses on the latter? If yes how? That’s really important to me otherwise a reviewer could claim the myelin differences we detect might be supported by cortical thickness variations and not myelin… Thank you and best, Damien > Glasser, Matthew <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Mon, 22 Oct 2018 12:57:43 -0700 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> > > Regression would be better than division. > Matt. > > From: > <freesurfer-boun...(a)nmr.mgh.harvard.edu <http://nmr.mgh.harvard.edu/><mailto:freesurfer-boun...@nmr.mgh.harvard.edu <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>> > on behalf of Damien MARIE <damien.ma <http://damien.ma/>...(a)unige.ch <http://unige.ch/><mailto:damien.ma...@unige.ch <mailto:damien.ma...@unige.ch>>> > Reply-To: Freesurfer support list > <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > Date: Monday, October 22, 2018 at 8:54 AM > To: "freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>" > <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > Subject: [Freesurfer] Myelinated cortical thickness ratio map > > > External Email - Use Caution > > Dear experts, > > I am working with R1 maps that I project on the surface. The goal is to look at > intra-cortical myelin. > > I detect interesting effects between two groups. Now I would like to compute > myelinated cortical thickness ratio maps, in order to control for the effect of > cortical thickness variations occurring with gyrification. > > Here is a paper where they describe a way to compute those myelinated cortical > thickness ratio map with MIPAV and the MPI-CBS toolbox : > https://www.ncbi.nlm.nih.gov/pubmed/29321232 <https://www.ncbi.nlm.nih.gov/pubmed/29321232> > « The proportional thickness of the myelinated part of the cortex in relation > to its overall thickness (myelinated cortical thickness) was computed with a > fuzzy classification technique combining information about radial and > tangential fibers. « > > 1- Is it possible to do the same in FreeSurfer? > > 2- What about dividing my individual myelin maps by the individual cortical > thickness maps? Is it possible to do that in FreeSurfer? SPM ImCalc would do > the job in the volume but I don’t know how I could do that in FreeSurfer. > > Any comments / other suggestions are welcome. > > Thank you and best, > > Damien >

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