Freesurfer

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30132 discussions

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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Re: [Freesurfer] Issues with hippo subfields / amygdala fixed
by Maksimovskiy, Arkadiy 17 Jan '18

17 Jan '18

Got it. Thank you so much for all the information. Best, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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Re: [Freesurfer] Hippocampal Sub-field volume units
by Iglesias Gonzalez, Eugenio 17 Jan '18

17 Jan '18

Short answer: yes, it’s cubic mm. -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Crawford, Anna" <CRAWFOA4(a)ccf.org> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, 17 January 2018 at 19:20 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Hippocampal Sub-field volume units Hello, i am using the hippocampal subfield segmentation. I am looking at the results in [lr]h.hippoSfVolumes-T1.v10.txt. I saw the following in the FAQs and was unsure of what the units were then in the .txt file. Does the .txt file give units in mm^3? * The sum of the number of voxels of a given structure multiplied by the volume of a voxel is not equal to the volume reported in [lr]h.hippoSfVolumes*.txt. This is because the volumes are computed upon a soft segmentation, rather than the discrete labels in [lr]h.hippoSfLabels*.mgz. This is the same that happens with the main recon-all stream: if you compute volumes by counting voxels in aseg.mgz, you don't get the values reported in aseg.stats. Thank you, Anna =================================== Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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Hippocampal Sub-field volume units
by Crawford, Anna 17 Jan '18

17 Jan '18

Hello, i am using the hippocampal subfield segmentation. I am looking at the results in [lr]h.hippoSfVolumes-T1.v10.txt. I saw the following in the FAQs and was unsure of what the units were then in the .txt file. Does the .txt file give units in mm^3? * The sum of the number of voxels of a given structure multiplied by the volume of a voxel is not equal to the volume reported in [lr]h.hippoSfVolumes*.txt. This is because the volumes are computed upon a soft segmentation, rather than the discrete labels in [lr]h.hippoSfLabels*.mgz. This is the same that happens with the main recon-all stream: if you compute volumes by counting voxels in aseg.mgz, you don't get the values reported in aseg.stats. Thank you, Anna =================================== Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

1 0

Issues with hippo subfields / amygdala fixed
by Maksimovskiy, Arkadiy 17 Jan '18

17 Jan '18

Dear Dr. Iglesias, Could you please let me know what the specific problems were that are fixed? I am asking because I have already applied this segmentation, and want to make sure that the data is valid. Thank you so much, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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