Freesurfer January 2018

freesurfer@nmr.mgh.harvard.edu

124 participants
195 discussions

PET partial volume correction
by John Anderson 18 Jan '18

18 Jan '18

Dear Dr Greeve, I interestingly read the manuscript "Different partial volume correction methods lead to different conclusions: An (18)F-FDG-PET study of aging" Thank you for publishing this data. I understood from this paper that he recommended stream for PVC is to correct the PET images using Muller-Gartner method then feed the corrected maps into three group level analyses: surface based for left and right hemispheres then for subcortical regions.. My question is about the subcortical analysis: To describe this analysis, is it a volumetric analysis for subcortical gray matter, or surface based? I am sorry if my questions is basics, I don't have good experience in freesurfer so I want to be sure that I am using the correct terms. Thanks you for any advice! John

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PET partial volume correction
by John Anderson 18 Jan '18

18 Jan '18

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mri_coreg
by John Anderson 18 Jan '18

18 Jan '18

Dear FS developers, Are there any versions of "mri_coreg" that allows to output the registered images. I mean flag "--out or -o" similar to spmregister? Thanks for any guidance John

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motion parameter in preprocessing stream
by Carme Uribe Codesal 18 Jan '18

18 Jan '18

Dear all FreeSurfer users, I was wondering if I can extract any parameter of movement from the recon-all processing using FreeSurfer 5.1. Thanks in advance! Kind regards, Carme

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aparcstats2table
by Stephanos Leandrou 18 Jan '18

18 Jan '18

Dear Freesurfer Developers, I want to use the asegstats2table and aparcstats2table for my research. First of all, my subjects (several hundreds) are not in the Freesurfer/Subjects directory and for each one I have run the recon-all command. For the asegstats2table command we know that the subjects list can be specified in one of four ways: 1. Specify each subject after -s * -s subject1 -s subject2 .. 2. specify all subjects after --subjects. * --subjects does not have to be the last argument. Eg: * --subjects subject1 subject2 ... 3. Specify each input file after -i * -i subject1/stats/aseg.stats -i subject2/stat/aseg.stats .. 4. Specify all the input stat files after --inputs. --inputs does not have * to be the last argument. Eg: * --inputs subject1/stats/aseg.stats subject2/stats/aseg.stats ... The first two methods assume the freesurfer directory structure. The last two are general and can be used with any file produced by mri_segstats regardless of whether it was created with recon-all or not..... According to 3 and 4 by changing -subjects to -i I was able to run the asegstats2table command for my subjects that are not in the Freesurfer directory structure with success. However, (and here comes my question) I cannot do the same for the aparcstats2table because there is no option (if I am not mistaken) to run the command for subjects outside the Freesurfer directory structure? In the aparcstats2table webpage mentions that the subjects list can be specified on either of two ways: 1. Specify each subject after a -s flag * -s subject1 -s subject2 ... --hemi lh 2. Specify all subjects after --subjects flag. --subjects does not have * to be the last argument. Eg: * --subject subject1 subject2 ... --hemi lh However, when I run the command (in the path of my subjects directory where the stats folder is) it comes with an error which says that it cannot find the stats file in the Freesurfer/directory which is expected...as my subjects are not in that directory. Thank you for your help !! Stephanos

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Cerebral cortex
by 郑凤莲 18 Jan '18

18 Jan '18

Hi FS experts, I am using Freesurfer 6.0 for cerebral cortex study. I want to study the relationship between cortical thickness and surface area, thickness and LGI, LGI and surface area, such as the following figure: How can I get these results? Is there any tutorial? I don't know how to do. I need your help. Thanks very much. Sincerely, Zheng

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Jittering Fixation Time
by Ashley Cole 18 Jan '18

18 Jan '18

Dear FreeSurfer Experts, I have a question about jittering the fixation point and how Freesurfer handles it. Is it ok to have different rest times in the paradigm file for FS-FAST pipeline? In the paradigm file, I am giving it an actual onset time and for the length of the rest block I am giving it a length that has been jittered and sometimes this length is a multiple of the TR and sometimes is not. Is this ok? Thank you, Ash

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ROI statistics and median values
by Helen Beaumont 18 Jan '18

18 Jan '18

I can use mri_segstats to get mean and std dev for values within a segmented image. Is there any way I can get median values?

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why freesurfer is not able to segment frontal cortex
by Vidhu Agrawal 18 Jan '18

18 Jan '18

Does freesurfer segments frontal cortex? If yes the how we can do that I have tried to do it by using the command :mri_binarize --i aseg.mgz --o ctx-lh-s_frontal_superior.nii --match 1156 mri_binarize --i aseg.mgz --o ctx-lh-s_frontal_inferior.nii --match 1154 mri_binarize --i aseg.mgz --o ctx-lh-s_frontal_middle.nii --match 1156 mri_binarize --i aseg.mgz --o ctx-lh-g_frontal_inf_operacula.nii --match 1106 mri_binarize --i aseg.mgz --o ctx-lh-g_frontal_inf_orbital.nii --match 1107 mri_binarize --i aseg.mgz --o ctx-lh-g_frontal_inf_triangula.nii --match 1108 mri_binarize --i aseg.mgz --o ctx-lh-g_frontal_middle.nii --match 1109 mri_binarize --i aseg.mgz --o ctx-lh-g_frontal_superior.nii --match 1110 but it is not segmenting any region Looking forward for your reply. Thanking you With regards vidhu agarwal

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Re: [Freesurfer] Visualisation left and right hemisphere
by Douglas Greve 18 Jan '18

18 Jan '18

Hi Ahmad, you can use mris_left_right_register to register the left and right hemis, then mris_apply_reg to map the left annot to the right (or other way around). ps. please remember to post to the FS list. Thanks! On 1/17/18 9:13 AM, Ahmad Mheich wrote: > /Hello, / > // > /Is it possible to combine the lh and rh annotation files into a > single //annotation file for visualisation? How? / > /Best regards/ > /Ahmad/

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Freesurfer January 2018