[Freesurfer] Fwd: extracting rois for connectivity analysis
Dear Freesurfer's I draw a roi to extract the cortical thickness for my two groups and that worked fine. Now I'm trying to export the very same roi to use it for further connectivity analysis. Can anyone please help me and tell me how to do it? Thanks in advance!! :-) Cheers Jutta ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] ADNI freesurfer annotation/labels file
Hi Tanya what kind of labels do you mean? If it is the cortical parcels they are in the label subdir in the *.annot files. cheers Bruce On Wed, 7 May 2014, Tanya wrote: Hi Freesurfers,I'd like to work with ADNI freesurfer data to do analysis on cortical segments, but could not find the annotation files for these studies. Where in the ADNI freesurfer files can I find the annotation/labels files containing the labels for each vertex on the cortical surfaces? Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Fwd: extracting rois for connectivity analysis
Hi Jutta we need more details - what format are you trying to conver the ROI to? What software are you planning to use to do the connectivity analysis? cheers Bruce On Thu, 8 May 2014, Jutta Ernst wrote: Dear Freesurfer's I draw a roi to extract the cortical thickness for my two groups and that worked fine. Now I'm trying to export the very same roi to use it for further connectivity analysis. Can anyone please help me and tell me how to do it? Thanks in advance!! :-) Cheers Jutta ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Fwd: extracting rois for connectivity analysis
Hi Nifti would be great and the software would be Data Processing Assistant for Resting-State fMRI (/DPARSF/). Cheers, Jutta On 05/08/2014 02:38 PM, Bruce Fischl wrote: Hi Jutta we need more details - what format are you trying to conver the ROI to? What software are you planning to use to do the connectivity analysis? cheers Bruce On Thu, 8 May 2014, Jutta Ernst wrote: Dear Freesurfer's I draw a roi to extract the cortical thickness for my two groups and that worked fine. Now I'm trying to export the very same roi to use it for further connectivity analysis. Can anyone please help me and tell me how to do it? Thanks in advance!! :-) Cheers Jutta ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Fwd: extracting rois for connectivity analysis
and what format is your ROI in? On Thu, 8 May 2014, Jutta Ernst wrote: Hi Nifti would be great and the software would be Data Processing Assistant for Resting-State fMRI (DPARSF). Cheers, Jutta On 05/08/2014 02:38 PM, Bruce Fischl wrote: Hi Jutta we need more details - what format are you trying to conver the ROI to? What software are you planning to use to do the connectivity analysis? cheers Bruce On Thu, 8 May 2014, Jutta Ernst wrote: Dear Freesurfer's I draw a roi to extract the cortical thickness for my two groups and that worked fine. Now I'm trying to export the very same roi to use it for further connectivity analysis. Can anyone please help me and tell me how to do it? Thanks in advance!! :-) Cheers Jutta ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Longitudinal design
Sorry for the repeat, wasn't sure whether this was received the first time. Tudor On 6 May 2014 19:55, Tudor Popescu tud...@gmail.com wrote: Dear FS list, I have structural data from a learning study (prepost-training scans, with 3 groups). Although the training was only one week, I'm guessing from an analysis point of view, this still qualifies as longitudinal. I want to check for - the main within-subjects effect of time point (prepost) - the main between-subjects effect of group (treatment A, treatment B, control), - the time x group interaction I intend to look at thickness, surface area, volume, and lGI. I read on the wikihttp://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessingthat FS is currently not optimal for longitudinal analyses. I intend my FreeSurfer analysis to supplement a VBM analysis done in FSL. In case it is in fact a good idea to do this, my questions (not covered in the 'longitudinal' wiki page) are: 1) Can QDEC be used for such an analysis, and if so, what would be different as compared to a cross-sectional (no temporal/within factor) study? 2) Also, is the pre-processing stage any different? 3) In FSL, for longitudinal designs you do stats on images obtained as the difference between consecutive time points. Does this have to be done in FreeSurfer as well, and if so, is it done at the recon-all level or only at the stats (QDEC) level? Thanks! Tudor ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Longitudinal design
Hi Tudor I'll leave ths stats question to Martin or Jorge, but I'm not sure why the wiki would say out longitudinal stream is not optimal. It is certainly as optimal as we have had the resources to make it, although there are a long list of things we would still like to do. cheers Bruce On Thu, 8 May 2014, Tudor Popescu wrote: Sorry for the repeat, wasn't sure whether this was received the first time. Tudor On 6 May 2014 19:55, Tudor Popescu tud...@gmail.com wrote: Dear FS list, I have structural data from a learning study (prepost-training scans, with 3 groups). Although the training was only one week, I'm guessing from an analysis point of view, this still qualifies as longitudinal. I want to check for * the main within-subjects effect of time point (prepost) * the main between-subjects effect of group (treatment A, treatment B, control), * the time x group interaction I intend to look at thickness, surface area, volume, and lGI. I read on the wiki that FS is currently not optimal for longitudinal analyses. I intend my FreeSurfer analysis to supplement a VBM analysis done in FSL. In case it is in fact a good idea to do this, my questions (not covered in the 'longitudinal' wiki page) are: 1) Can QDEC be used for such an analysis, and if so, what would be different as compared to a cross-sectional (no temporal/within factor) study? 2) Also, is the pre-processing stage any different? 3) In FSL, for longitudinal designs you do stats on images obtained as the difference between consecutive time points. Does this have to be done in FreeSurfer as well, and if so, is it done at the recon-all level or only at the stats (QDEC) level? Thanks! Tudor ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Fwd: extracting rois for connectivity analysis
then you probably want to use mri_label2vol to sample it into the volume. If the output name has the extension .nii it will be in nifti format cheers Bruce On Thu, 8 May 2014, Jutta Ernst wrote: It's a label file... On 05/08/2014 02:56 PM, Bruce Fischl wrote: and what format is your ROI in? On Thu, 8 May 2014, Jutta Ernst wrote: Hi Nifti would be great and the software would be Data Processing Assistant for Resting-State fMRI (DPARSF). Cheers, Jutta On 05/08/2014 02:38 PM, Bruce Fischl wrote: Hi Jutta we need more details - what format are you trying to conver the ROI to? What software are you planning to use to do the connectivity analysis? cheers Bruce On Thu, 8 May 2014, Jutta Ernst wrote: Dear Freesurfer's I draw a roi to extract the cortical thickness for my two groups and that worked fine. Now I'm trying to export the very same roi to use it for further connectivity analysis. Can anyone please help me and tell me how to do it? Thanks in advance!! :-) Cheers Jutta ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Fwd: extracting rois for connectivity analysis
It's a label file... On 05/08/2014 02:56 PM, Bruce Fischl wrote: and what format is your ROI in? On Thu, 8 May 2014, Jutta Ernst wrote: Hi Nifti would be great and the software would be Data Processing Assistant for Resting-State fMRI (DPARSF). Cheers, Jutta On 05/08/2014 02:38 PM, Bruce Fischl wrote: Hi Jutta we need more details - what format are you trying to conver the ROI to? What software are you planning to use to do the connectivity analysis? cheers Bruce On Thu, 8 May 2014, Jutta Ernst wrote: Dear Freesurfer's I draw a roi to extract the cortical thickness for my two groups and that worked fine. Now I'm trying to export the very same roi to use it for further connectivity analysis. Can anyone please help me and tell me how to do it? Thanks in advance!! :-) Cheers Jutta ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] 2x3 ANOVA question
Hi all, I am trying to run 2x3 factorial model correcting for age, sex and intracranial volume. Just to give you insight in my data I have my fsgd file as GroupDescriptorFile 1 Title DOSS analysis 2x3 factorial Class MaleGroup1Low Class MaleGroup1Medium Class MaleGroup1High Class MaleGroup2Low Class MaleGroup2Medium Class MaleGroup2HighClass FemaleGroup1Low Class FemaleGroup1Medium Class FemaleGroup1High Class FemaleGroup2Low Class FemaleGroup2Medium Class FemaleGroup2High Variables Age normVol Input SUB001 MaleGroup1Low 18 0.4 And also my contrast files as Group1Group2.mtx [1 1 1 -1 -1 -1 1 1 1 -1 -1 -1]/3 MainEffectState.mtx 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 HighvLow.mtx -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0.5 HighvMed.mtx 0 -0.5 0.5 0 -0.5 0.5 0 -0.5 0.5 0 -0.5 0.5 GroupxState-interaction.mtx 0.5 -0.5 0 -0.5 0 0.5 0.5 -0.5 0 -0.5 0 0.5 0.5 0 -0.5 -0.5 0 0.5 0.5 0 -0.5 -0.5 0 0.5 I'd appreciate if anyone could please let me know that my design is correct. Thanks for help. -Sabin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Fwd: extracting rois for connectivity analysis
Thank you, that solved it :-)cheers Am 08.05.2014 um 15:56 schrieb Bruce Fischl fis...@nmr.mgh.harvard.edu: then you probably want to use mri_label2vol to sample it into the volume. If the output name has the extension .nii it will be in nifti format cheers Bruce On Thu, 8 May 2014, Jutta Ernst wrote: It's a label file... On 05/08/2014 02:56 PM, Bruce Fischl wrote: and what format is your ROI in? On Thu, 8 May 2014, Jutta Ernst wrote: Hi Nifti would be great and the software would be Data Processing Assistant for Resting-State fMRI (DPARSF). Cheers, Jutta On 05/08/2014 02:38 PM, Bruce Fischl wrote: Hi Jutta we need more details - what format are you trying to conver the ROI to? What software are you planning to use to do the connectivity analysis? cheers Bruce On Thu, 8 May 2014, Jutta Ernst wrote: Dear Freesurfer's I draw a roi to extract the cortical thickness for my two groups and that worked fine. Now I'm trying to export the very same roi to use it for further connectivity analysis. Can anyone please help me and tell me how to do it? Thanks in advance!! :-) Cheers Jutta ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images
Hi Emil how do the surfaces look before you apply the T2 deformation? And how do they look visualized over the T2 instead of the T1? cheers Bruce On Thu, 8 May 2014, Emil H.J. Nijhuis wrote: Hi, I have been using Freesurfer v5.3 to perform surface reconstruct for 1mm isotropic T1 (MPRAGE) and T2 (SPACE) weighted images from a Siemens 3T Trio scanner with a 32-channel head coil. Unfortunately for half of my subjects I receive an rather odd pial surface artefact, while the 'white' surfaces do not suffer from the same issue. The command line I have used was: recon-all -all -subjid subjectid -T2 subjectdir/mri/orig/T2.mgz -T2pial -3T Are you familiar with this issue and do you have some advice for me? Thank you very much for your help. Yours sincerely, Emil -- -- Emil H.J. Nijhuis, PhD Researcher - Division of Diagnostic and Interventional Neuroradiology University Hospital Basel Petersgraben 4 CH 4031 Basel Switzerland ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Information on automatic segmentation method
Hi, From what I understand, Freesurfer's automatic segmentation pipeline is partly based on a training set of subjects manually segmented. Is there a way to get more information on which protocol/guideline was used to manually segment (or define anatomical boundaries) these subjects at the baseline? I am unable to find this information... Thank you in advance for your assistance! Dorothée. -- *PhD candidate in Clinical Psychology* *McGill University* *McGill Centre for Studies in Aging* *Montreal, CANADA* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Information on automatic segmentation method
Hi, From what I understand, Freesurfer's automatic segmentation pipeline is partly based on a training set of subjects manually segmented. Is there a way to get more information on which protocol/guideline was used to manually segment (or define anatomical boundaries) these subjects at the baseline? I am unable to find this information... Thank you in advance for your assistance! Dorothée. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Information on automatic segmentation method
Hi Dorothy yes, this is referred to in our 2002 Neuron paper - we use the CMA segmentation procedure/definitions (see the references in that paper) cheers Bruce On Thu, 8 May 2014, dorothee schoemaker wrote: Hi, From what I understand, Freesurfer's automatic segmentation pipeline is partly based on a training set of subjects manually segmented. Is there a way to get more information on which protocol/guideline was used to manually segment (or define anatomical boundaries) these subjects at the baseline? I am unable to find this information... Thank you in advance for your assistance! Dorothée. -- PhD candidate in Clinical PsychologyMcGill University McGill Centre for Studies in Aging Montreal, CANADA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] nonlinear models in longitudinal analysis
Dear Freesurfer experts, I am attempting to do a longitudinal analysis of cortical thickness with 3 timepoints. So far, I have successfully completed the analysis for long_mris_slopes comparing timepoint 1 to timepoint 2, timepoint 2 to timepoint 3, and a linear increase for timepoint 1 to 2 to 3. However, I am primarily interested in finding regions which show a) an increase between timepoint 1 and 2, but no difference between 2 and 3, and b) no difference between timepoint 1 and 2, but an increase between 2 and 3. Would the correct way of 'modelling' these two in the qdec file be: a) fsid fsid-base years day1 base 0 day2 base 3 day3 base 3 and b) fsid fsid-base years day1 base 0 day2 base 0 day3 base 3 All the best, Jodie - --- Jodie Davies-Thompson, Postdoctoral Fellow Department of Ophthalmology Visual Sciences UBC/VGH Eye Care Centre 2550 Willow Street Vancouver, BC, V5Z 3N9 Canada Tel: 604-875-4111 ext 69003 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] flash v.s. mprage
looking at the docs available it seems that in general flash is prefered but it seems that for cortical thickness studies you may still favor the mprage ? all with good parameter setting of course. thanks in advance for any clarifying comments you may have Greg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
