Re: [Freesurfer] QDEC/mri_glmfit questions
External Email - Use Caution Hi Doug, Thank you for the advice! I tried plugging the output of aparc2stats into mri_glmfit both in tandem with —y (mri_preproc_output).mgh as well as on its own and got an error message from mri_reshape saying the elements cannot be changed nv1=163842, nv1=2. This was an iteration of the table with one data column for the thickness of an ROI, however, I also got the same error with the full table. This is also the same table we used in SPSS for a linear regression there. Terminal inputs: mri_glmfit —y lh.thickness.inflammatory.10.mgh —fsgd inflammatory_markers.fsgd —C Inflammatory_group.mtx —C group_inflammatory.mtx —surf fsaverage —table entorhinal_table.dat —label entorhinal.label —glmdir Inflammatory_entorhinal.lh.thickness.10.glmdir mri_glmfit —fsgd inflammatory_markers.fsgd —C Inflammatory_group.mtx —C group_inflammatory.mtx —surf fsaverage —table aparc_table.dat —label entorhinal.label —glmdir Inflammatory_entorhinal.lh.thickness.10.glmdir Thanks! Erin > On Feb 18, 2021, at 11:15 AM, Erin Moe wrote: > > Hi Freesurfer experts, > I’ve been running mri_glmfit and QDEC to investigate the effect of > inflammatory markers on cortical thickness and don’t really get much. > However, when I extract the cortical thickness values (with > aparc/asegstats2table) and run a linear regression with those same > inflammatory markers in SPSS, I get several significant results. I’m assuming > it might be due to me setting up the QDEC/mri_glmfit analysis wrong. > > For QDEC I have a two column .dat file with the subject IDs in the FSID > column and the inflammatory markers for each participant in the other column > and running the QDEC thickness analysis on that and I don’t get much in terms > of results. > > For mri_glmfit I used an FSGD file set up just like the .dat file for QDEC > with the exception of formatting. However, we wanted to constrain the > analysis to an ROI (entorhinal in this case), I ran mris_preproc with the > following command: > mris_preproc —fsgd inflammatory_markers.fsgd —cache-in > thickness.fwhm10.fsaverage —target fsaverage —hemi lh —out > lh.thickness.inflammatory.10.mgh > > Then fed that output into mri_glmfit as: > mri_glmfit —y lh.thickness.inflammatory.10.mgh —fsgd > inflammatory_markers.fsgd —C Inflammatory_group.mtx —C group_inflammatory.mtx > —surf fsaverage —label entorhinal.label —glmdir > Inflammatory_entorhinal.lh.thickness.10.glmdir > The results from this look the same as the QDEC analysis but just masked out > for the entorhinal ROI. So, to constrain the analysis to the ROI, I ran a > Monte Carlo correction with mri_surfcluster. > > So a few questions: > Would running mri_surfcluster on the sig.mgh output from the mri_glmfit > analysis actually constrain the analysis to the ROI specified? > > How can I get my results to match that of what I’m seeing in SPSS? > > Is my analysis set up correctly for what I’m trying to do? > > > > Thank you in advance for your patience with this lengthy inquiry. > > Best, > Erin > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] QDEC/mri_glmfit questions
External Email - Use Caution Hi Freesurfer experts, I’ve been running mri_glmfit and QDEC to investigate the effect of inflammatory markers on cortical thickness and don’t really get much. However, when I extract the cortical thickness values (with aparc/asegstats2table) and run a linear regression with those same inflammatory markers in SPSS, I get several significant results. I’m assuming it might be due to me setting up the QDEC/mri_glmfit analysis wrong. For QDEC I have a two column .dat file with the subject IDs in the FSID column and the inflammatory markers for each participant in the other column and running the QDEC thickness analysis on that and I don’t get much in terms of results. For mri_glmfit I used an FSGD file set up just like the .dat file for QDEC with the exception of formatting. However, we wanted to constrain the analysis to an ROI (entorhinal in this case), I ran mris_preproc with the following command: mris_preproc —fsgd inflammatory_markers.fsgd —cache-in thickness.fwhm10.fsaverage —target fsaverage —hemi lh —out lh.thickness.inflammatory.10.mgh Then fed that output into mri_glmfit as: mri_glmfit —y lh.thickness.inflammatory.10.mgh —fsgd inflammatory_markers.fsgd —C Inflammatory_group.mtx —C group_inflammatory.mtx —surf fsaverage —label entorhinal.label —glmdir Inflammatory_entorhinal.lh.thickness.10.glmdir The results from this look the same as the QDEC analysis but just masked out for the entorhinal ROI. So, to constrain the analysis to the ROI, I ran a Monte Carlo correction with mri_surfcluster. So a few questions: Would running mri_surfcluster on the sig.mgh output from the mri_glmfit analysis actually constrain the analysis to the ROI specified? How can I get my results to match that of what I’m seeing in SPSS? Is my analysis set up correctly for what I’m trying to do? Thank you in advance for your patience with this lengthy inquiry. Best, Erin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Constraining analysis to ROI
External Email - Use Caution Hi Doug, Thanks for the prompt reply. I did use the label option in mri_glmfit, but it seemed to just show the same results as the whole brain analysis but for only in the region defined by the label. When I load the sig scalar into QDEC from the label analysis as well as sig scalar from the whole brain analysis, the results looks exactly the same within the region that I have labeled. Wouldn’t constraining the analysis to just the region defined by the label potentially increase the power and therefore the significance? When I compare the significant clusters from both analyses they show the same values. My apologies if this is not the case, I am a bit rusty with my stats. Thanks again for all the help! Erin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Constraining analysis to ROI
External Email - Use Caution Hello Freesurfer experts, Is there a way to constrain an analysis to a label or ROI in QDEC? I have a group analysis looking at the effect of inflammatory markers on thickness however, I’d like to have the analysis be constrained within an ROI rather than whole brain to increase the power. I specified a label in mir_glmfit but the analysis seems to just mask out the rest of the brain rather than constraining to the ROI. Thank you for all your help! Erin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Thalamic nuclei in FSL
External Email - Use Caution Hi Doug, That would do it. Thanks! However, I ran bbregister, got out the register.dat file, input that into the vol2subfield command and now it’s giving me an error stating: "dst or src volume is invalid. Inverse likely wrong…error: mir_concatenate_lta: unknown transform type for LTA1. My apologies if these are newbie mistakes, I’m still learning my way around Freesurfer. Thanks! Erin On Jul 30, 2020, at 12:50 PM, Erin Moe mailto:erin@colorado.edu>> wrote: Hi Doug, Thanks for the quick response. I've attached a text file of the terminal output after running vol2subfield with the --dubug option. Thanks! Erin From: Erin Moe mailto:erin@colorado.edu>> Sent: Tuesday, July 28, 2020 11:26 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Thalamic nuclei in FSL Hi Freesurfer experts, I ran segmentThalamicNuclei on my dataset and would like to use the segmentations on BOLD data in FSL using Featquery. I tried running vol2subfield but got an error: “set: Variable name must contain alphanumeric characters. I’ve tried a mired of other things to get the thalamic nuclei output into the mean_func.nii.gz space but haven’t had much success. What would you recommend I try? Terminal input for vol2subfield (note the dashes are double, my email client automatically changes them to single dashes): vol2subfield —i mean_func.nii.gz —reg $subject —$subject/mri/ThalamicNuclei.v12.T1.mgz —BOLD_thalamus.mgz Thanks! Erin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Thalamic nuclei in FSL
External Email - Use Caution Hi Doug, Thanks for the quick response. I've attached a text file of the terminal output after running vol2subfield with the --dubug option. Thanks! Erin From: Erin Moe Sent: Tuesday, July 28, 2020 11:26 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Thalamic nuclei in FSL Hi Freesurfer experts, I ran segmentThalamicNuclei on my dataset and would like to use the segmentations on BOLD data in FSL using Featquery. I tried running vol2subfield but got an error: “set: Variable name must contain alphanumeric characters. I’ve tried a mired of other things to get the thalamic nuclei output into the mean_func.nii.gz space but haven’t had much success. What would you recommend I try? Terminal input for vol2subfield (note the dashes are double, my email client automatically changes them to single dashes): vol2subfield —i mean_func.nii.gz —reg $subject —$subject/mri/ThalamicNuclei.v12.T1.mgz —BOLD_thalamus.mgz Thanks! Erin vol2subfield --debug --i mean_func.nii.gz --reg M80301954_20190314 --sf /pl/active/ics/data/projects/hutchisonlab/studies/alcohol/AIM/FreeSurfer_data/fs_files/M80301954_20190314/mri/ThalamicNuclei.v12.T1.mgz --o BOLD_thalamus.mgz >> vol2subfield_debug.txt set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 8 != 0 ) set flag = $argv[1] ; shift ; set flag = --i shift switch ( $flag ) switch ( --i ) if ( $#argv < 1 ) goto arg1err ; if ( 7 < 1 ) goto arg1err set invol = $argv[1] ; shift ; set invol = mean_func.nii.gz shift breaksw breaksw end end while ( $#argv != 0 ) while ( 6 != 0 ) set flag = $argv[1] ; shift ; set flag = --reg shift switch ( $flag ) switch ( --reg ) if ( $#argv < 1 ) goto arg1err ; if ( 5 < 1 ) goto arg1err set reg = $argv[1] ; shift ; set reg = M80301954_20190314 shift breaksw breaksw end end while ( $#argv != 0 ) while ( 4 != 0 ) set flag = $argv[1] ; shift ; set flag = --sf shift switch ( $flag ) switch ( --sf ) if ( $#argv < 1 ) goto arg1err ; if ( 3 < 1 ) goto arg1err set subfieldvol = $argv[1] ; shift ; set subfieldvol = /pl/active/ics/data/projects/hutchisonlab/studies/alcohol/AIM/FreeSurfer_data/fs_files/M80301954_20190314/mri/ThalamicNuclei.v12.T1.mgz shift breaksw breaksw end end while ( $#argv != 0 ) while ( 2 != 0 ) set flag = $argv[1] ; shift ; set flag = --o shift switch ( $flag ) switch ( --o ) if ( $#argv < 1 ) goto arg1err ; if ( 1 < 1 ) goto arg1err set outvol = $argv[1] ; shift ; set outvol = BOLD_thalamus.mgz shift breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 ) goto parse_args_return ; goto parse_args_return goto check_params ; goto check_params if ( $#invol == 0 ) then if ( 1 == 0 ) then if ( $#subfieldvol == 0 ) then if ( 1 == 0 ) then if ( $#reg == 0 ) then if ( 1 == 0 ) then set subject = `reg2subject --r $reg` set subject = `reg2subject --r $reg` reg2subject --r M80301954_20190314 set orig = $SUBJECTS_DIR/$subject/mri/orig.mgz set orig = /pl/active/ics/data/projects/hutchisonlab/studies/alcohol/AIM/FreeSurfer_data/fs_files/ERROR: cannot find M80301954_20190314/mri/orig.mgz set: Variable name must contain alphanumeric characters. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Thalamic nuclei in FSL
External Email - Use Caution Hi Freesurfer experts, I ran segmentThalamicNuclei on my dataset and would like to use the segmentations on BOLD data in FSL using Featquery. I tried running vol2subfield but got an error: “set: Variable name must contain alphanumeric characters. I’ve tried a mired of other things to get the thalamic nuclei output into the mean_func.nii.gz space but haven’t had much success. What would you recommend I try? Terminal input for vol2subfield (note the dashes are double, my email client automatically changes them to single dashes): vol2subfield —i mean_func.nii.gz —reg $subject —$subject/mri/ThalamicNuclei.v12.T1.mgz —BOLD_thalamus.mgz Thanks! Erin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
