Dear FreeSurfer experts,
I'm trying to run a mri_glmfit on my first time point (out of 3). I ran the glm with this: mri_glmfit --table $SUBJECTS_DIR/aparcs_stats_sc1.txt --fsgd $SUBJECTS_DIRfsgd_sc1.txt --C $SUBJECTS_DIR/group.mtx --surf 87kids_template lh --cortex --glmdir $SUBJECTS_DIR/glm/lh.thick_group.glmdir
So far so good :)
Now when I try to apply the Monte Carlo correction with this: mri_glmfit-sim --glmdir $SUBJECTS_DIR/qdec/87kids/glm/lh.thick_group.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor --cache 3.0 neg --cwp 0.05 --2spaces
I get the error "fwhm: Undefined variable."
So I tried to run the glmfit with the --y flag and use the lh.thickness_sm10.mgh file but I created that when registering and smoothing ALL my time points to the template, so I get this error: "ERROR: dimension mismatch between y and X. y has 224 inputs, X has 72 rows."
I have looked at mri_glmfit-sim --help but there seems to be no flag for fwhm only an overwriting one.
Should I register and smooth the data again for the separate time points or is there another way to deal with that? What could I do to correct my glm data?
Cheers, Clara
Hi Martin,
thanks for your reply.
I have two further questions on that matter:
1. I opened the stacked file (lh.thickness_sm10.mgh) in matlab but there is no column for subject-id or anything to give me a hint which line is which subject. Is there a way to find that out? Is it in the same order as the subjects in the qdec table I gave mris_preproc as input?
2. I compared the output of mris_preproc and mris_surf2surf with the recon-all --qcache. They seem to be doing different things judging by the output but in the terminal it tells me that --qcache is also using preproc and surf2surf. However with --qcache I get the smoothed registration for each measure per subject (e.g. lh.thickness.fwhm10.87kids_template.mgh) and with preproc and surf2surf I get the stacked file (i.e. lh.thickness_sm10.mgh). Can you tell me what the difference between those two processes is? Are they overlapping in some steps or something like that?
Cheers, Clara
----- Ursprüngliche Mail ----- Von: "mreuter" mreuter@nmr.mgh.harvard.edu An: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 13. April 2016 16:39:18 Betreff: Re: [Freesurfer] correcting mri_glmfit results
Hi Clara, You need to register and smooth again for only the first time point. You could also open the full stack in Matlab, select the entries of your first time point and write it out again.
Best Martin
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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They are doing the same thing. If you stack the lh.thickness.fwhm10.87kids_template.mgh together into one file you should get the same thing as the output of mris_preproc. With mris_preproc, you have to keep track of the order of the subjects as specified in the --f or --fsgd options
On 04/14/2016 12:08 PM, Clara Kühn wrote:
Hi Martin,
thanks for your reply.
I have two further questions on that matter:
I opened the stacked file (lh.thickness_sm10.mgh) in matlab but there is no column for subject-id or anything to give me a hint which line is which subject. Is there a way to find that out? Is it in the same order as the subjects in the qdec table I gave mris_preproc as input?
I compared the output of mris_preproc and mris_surf2surf with the recon-all --qcache. They seem to be doing different things judging by the output but in the terminal it tells me that --qcache is also using preproc and surf2surf. However with --qcache I get the smoothed registration for each measure per subject (e.g. lh.thickness.fwhm10.87kids_template.mgh) and with preproc and surf2surf I get the stacked file (i.e. lh.thickness_sm10.mgh). Can you tell me what the difference between those two processes is? Are they overlapping in some steps or something like that?
Cheers, Clara
----- Ursprüngliche Mail ----- Von: "mreuter" mreuter@nmr.mgh.harvard.edu An: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 13. April 2016 16:39:18 Betreff: Re: [Freesurfer] correcting mri_glmfit results
Hi Clara, You need to register and smooth again for only the first time point. You could also open the full stack in Matlab, select the entries of your first time point and write it out again.
Best Martin
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
Awesome, thank you! Cheers, Clara
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Donnerstag, 14. April 2016 18:19:53 Betreff: Re: [Freesurfer] correcting mri_glmfit results
They are doing the same thing. If you stack the lh.thickness.fwhm10.87kids_template.mgh together into one file you should get the same thing as the output of mris_preproc. With mris_preproc, you have to keep track of the order of the subjects as specified in the --f or --fsgd options
On 04/14/2016 12:08 PM, Clara Kühn wrote:
Hi Martin,
thanks for your reply.
I have two further questions on that matter:
I opened the stacked file (lh.thickness_sm10.mgh) in matlab but there is no column for subject-id or anything to give me a hint which line is which subject. Is there a way to find that out? Is it in the same order as the subjects in the qdec table I gave mris_preproc as input?
I compared the output of mris_preproc and mris_surf2surf with the recon-all --qcache. They seem to be doing different things judging by the output but in the terminal it tells me that --qcache is also using preproc and surf2surf. However with --qcache I get the smoothed registration for each measure per subject (e.g. lh.thickness.fwhm10.87kids_template.mgh) and with preproc and surf2surf I get the stacked file (i.e. lh.thickness_sm10.mgh). Can you tell me what the difference between those two processes is? Are they overlapping in some steps or something like that?
Cheers, Clara
----- Ursprüngliche Mail ----- Von: "mreuter" mreuter@nmr.mgh.harvard.edu An: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 13. April 2016 16:39:18 Betreff: Re: [Freesurfer] correcting mri_glmfit results
Hi Clara, You need to register and smooth again for only the first time point. You could also open the full stack in Matlab, select the entries of your first time point and write it out again.
Best Martin
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
How would I stack them? I found --do-stack only as flag during the registering and smoothing but not as a command itself. Thanks, Clara
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Donnerstag, 14. April 2016 18:19:53 Betreff: Re: [Freesurfer] correcting mri_glmfit results
They are doing the same thing. If you stack the lh.thickness.fwhm10.87kids_template.mgh together into one file you should get the same thing as the output of mris_preproc. With mris_preproc, you have to keep track of the order of the subjects as specified in the --f or --fsgd options
On 04/14/2016 12:08 PM, Clara Kühn wrote:
Hi Martin,
thanks for your reply.
I have two further questions on that matter:
I opened the stacked file (lh.thickness_sm10.mgh) in matlab but there is no column for subject-id or anything to give me a hint which line is which subject. Is there a way to find that out? Is it in the same order as the subjects in the qdec table I gave mris_preproc as input?
I compared the output of mris_preproc and mris_surf2surf with the recon-all --qcache. They seem to be doing different things judging by the output but in the terminal it tells me that --qcache is also using preproc and surf2surf. However with --qcache I get the smoothed registration for each measure per subject (e.g. lh.thickness.fwhm10.87kids_template.mgh) and with preproc and surf2surf I get the stacked file (i.e. lh.thickness_sm10.mgh). Can you tell me what the difference between those two processes is? Are they overlapping in some steps or something like that?
Cheers, Clara
----- Ursprüngliche Mail ----- Von: "mreuter" mreuter@nmr.mgh.harvard.edu An: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 13. April 2016 16:39:18 Betreff: Re: [Freesurfer] correcting mri_glmfit results
Hi Clara, You need to register and smooth again for only the first time point. You could also open the full stack in Matlab, select the entries of your first time point and write it out again.
Best Martin
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
mri_concat
On 04/15/2016 08:17 AM, Clara Kühn wrote:
How would I stack them? I found --do-stack only as flag during the registering and smoothing but not as a command itself. Thanks, Clara
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Donnerstag, 14. April 2016 18:19:53 Betreff: Re: [Freesurfer] correcting mri_glmfit results
They are doing the same thing. If you stack the lh.thickness.fwhm10.87kids_template.mgh together into one file you should get the same thing as the output of mris_preproc. With mris_preproc, you have to keep track of the order of the subjects as specified in the --f or --fsgd options
On 04/14/2016 12:08 PM, Clara Kühn wrote:
Hi Martin,
thanks for your reply.
I have two further questions on that matter:
I opened the stacked file (lh.thickness_sm10.mgh) in matlab but there is no column for subject-id or anything to give me a hint which line is which subject. Is there a way to find that out? Is it in the same order as the subjects in the qdec table I gave mris_preproc as input?
I compared the output of mris_preproc and mris_surf2surf with the recon-all --qcache. They seem to be doing different things judging by the output but in the terminal it tells me that --qcache is also using preproc and surf2surf. However with --qcache I get the smoothed registration for each measure per subject (e.g. lh.thickness.fwhm10.87kids_template.mgh) and with preproc and surf2surf I get the stacked file (i.e. lh.thickness_sm10.mgh). Can you tell me what the difference between those two processes is? Are they overlapping in some steps or something like that?
Cheers, Clara
----- Ursprüngliche Mail ----- Von: "mreuter" mreuter@nmr.mgh.harvard.edu An: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 13. April 2016 16:39:18 Betreff: Re: [Freesurfer] correcting mri_glmfit results
Hi Clara, You need to register and smooth again for only the first time point. You could also open the full stack in Matlab, select the entries of your first time point and write it out again.
Best Martin
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
Looks like you are analyzing a table of data (ie, ROI analysis). In this case you cannot use clusterwise correction because you cannot form clusters of voxels when you don't have a voxel-wise analysis! You can do a bonferroni or FDR correction. You can get an FDR program from here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_fdr doug
On 4/13/16 8:40 AM, Clara Kühn wrote:
Dear FreeSurfer experts,
I'm trying to run a mri_glmfit on my first time point (out of 3). I ran the glm with this: mri_glmfit --table $SUBJECTS_DIR/aparcs_stats_sc1.txt --fsgd $SUBJECTS_DIRfsgd_sc1.txt --C $SUBJECTS_DIR/group.mtx --surf 87kids_template lh --cortex --glmdir $SUBJECTS_DIR/glm/lh.thick_group.glmdir
So far so good :)
Now when I try to apply the Monte Carlo correction with this: mri_glmfit-sim --glmdir $SUBJECTS_DIR/qdec/87kids/glm/lh.thick_group.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor --cache 3.0 neg --cwp 0.05 --2spaces
I get the error "fwhm: Undefined variable."
So I tried to run the glmfit with the --y flag and use the lh.thickness_sm10.mgh file but I created that when registering and smoothing ALL my time points to the template, so I get this error: "ERROR: dimension mismatch between y and X. y has 224 inputs, X has 72 rows."
I have looked at mri_glmfit-sim --help but there seems to be no flag for fwhm only an overwriting one.
Should I register and smooth the data again for the separate time points or is there another way to deal with that? What could I do to correct my glm data?
Cheers, Clara
freesurfer@nmr.mgh.harvard.edu
-
Clara Kühn -
Douglas Greve -
Douglas N Greve
-
Martin Reuter