Linda Zhang wrote:
Hi Doug,
Thanks for the clarification. If I were to add another two class variables (patient and subject, for example) and I wanted to see if they affected thickness, assuming they come after gender in the fsgd file, would the contrasts then be [0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0]?
Sorry, I can't remember what your design is (I answer a lot of emails and they often blend together). Can you refresh my memory?
From the powerpoint slides, there's an example where two contrast matrices are used (age, gender), what kind of output would that produce?
It would produce results (p-values, eg) for each of the contrasts. This allows you to run one command instead of one for each contrast.
/home/virtualuser/freesurfer/subjects/lh.MMSE-AD.thickness.00.mgh doesn't exist, I'm not sure why...
Your mris_preproc failed or you are not in the directory that has this file. doug
Cheers, Linda
On 3 December 2011 01:26, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
does /home/virtualuser/freesurfer/subjects/lh.MMSE-AD.thickness.00.mgh exist? doug Linda Zhang wrote: Dear all, I think I figured out the contrasts (I'm using [0 0 0 0 0.5 0.5 0 0]...is that correct?) but I've come across an error when trying to do the next step in the tutorial. I didn't cache the data during recon-all, so I ran the following: mris_preproc --fsgd MMSE-AD.fsgd --target fsaverage --hemi lh --meas thickness --out lh.MMSE-AD.thickness.00.mgh It seemed to run smoothly (I've attached the log below) so I ran the next step: mri_surf2surf --hemi lh --s fsaverage --sval lh.MMSE-AD.thickness.00.mgh --fwhm 10 --cortex --tval lh.MMSE-AD.thickness.10.mgh I got the following error: Reading source surface reg /home/virtualuser/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Loading source data mghRead(/home/virtualuser/freesurfer/subjects/lh.MMSE-AD.thickness.00.mgh, -1): could not open file ERROR: could not read lh.MMSE-AD.thickness.00.mgh as type 3 Can anyone tell me where the problem is? Thanks! Cheers, Linda The log for mris_preproc (truncated to the last subject and last line): --------------------------------------------------- #@# 12/12 avo1249 Fri Dec 2 18:20:04 HKT 2011 -------------- ----------------------- mri_surf2surf --srcsubject avo1249 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.18275/avo1249.12.mgh --sval /home/virtualuser/freesurfer/subjects/avo1249/surf/lh.thickness --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = avo1249 srcval = /home/virtualuser/freesurfer/subjects/avo1249/surf/lh.thickness srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.18275/avo1249.12.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /home/virtualuser/freesurfer/subjects/avo1249/surf/lh.sphere.reg Loading source data Reading curvature file /home/virtualuser/freesurfer/subjects/avo1249/surf/lh.thickness Reading target surface reg /home/virtualuser/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (121128) Reverse Loop had 15750 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 151248, nTrgMulti = 12594, MnTrgMultiHits = 2.2506 nSrc121 = 78171, nSrcLost = 0, nSrcMulti = 42957, MnSrcMultiHits = 2.36099 Saving target data Saving to ./tmp.mris_preproc.18275/avo1249.12.mgh ----------------------- mri_concat ./tmp.mris_preproc.18275/avo0015.1.mgh ./tmp.mris_preproc.18275/avo0260.2.mgh ./tmp.mris_preproc.18275/avo0403.3.mgh ./tmp.mris_preproc.18275/avo0441.4.mgh ./tmp.mris_preproc.18275/avo0493.5.mgh ./tmp.mris_preproc.18275/avo0622.6.mgh ./tmp.mris_preproc.18275/avo0677.7.mgh ./tmp.mris_preproc.18275/avo0920.8.mgh ./tmp.mris_preproc.18275/avo1086.9.mgh ./tmp.mris_preproc.18275/avo1206.10.mgh ./tmp.mris_preproc.18275/avo1241.11.mgh ./tmp.mris_preproc.18275/avo1249.12.mgh --o lh.MMSE-AD.thickness.00.mgh On 2 December 2011 11:42, Linda Zhang <lzhang87@gmail.com <mailto:lzhang87@gmail.com> <mailto:lzhang87@gmail.com <mailto:lzhang87@gmail.com>>> wrote: Dear all, I have a bit of an amateur question. I've read the slides and tutorial for group analysis, but I'm still confused about the contrasts. I made my fsgd file, which contains two groups: M and F. I also have three continuous variables: Age, MMSE, Education. I would like to test whether thickness is correlated with MMSE scores, after controlling for gender, age, and education. What should my contrast file be in this case? Thanks for the help! Cheers, Linda ------------------------------------------------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> 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.
Hi Doug,
Sure, my fsgd file contained two groups originally, M and F. I had three continuous variables, which were Age, MMSE, Education. I wanted to test whether thickness is correlated with MMSE scores after controlling for gender, age and education. I now want to add two more class variables (patient and volunteer), and see if they affect thickness. My question was asking if the contrasts in this case would be [0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0]?
I tried mris_preproc again with a different group, and that worked fine, so maybe it was just a fluke. Thanks!
Cheers, Linda
On 5 December 2011 23:10, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Linda Zhang wrote:
Hi Doug,
Thanks for the clarification. If I were to add another two class variables (patient and subject, for example) and I wanted to see if they affected thickness, assuming they come after gender in the fsgd file, would the contrasts then be [0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0]?
Sorry, I can't remember what your design is (I answer a lot of emails and they often blend together). Can you refresh my memory?
From the powerpoint slides, there's an example where two contrast
matrices are used (age, gender), what kind of output would that produce?
It would produce results (p-values, eg) for each of the contrasts. This allows you to run one command instead of one for each contrast.
/home/virtualuser/freesurfer/**subjects/lh.MMSE-AD.thickness.**00.mgh doesn't exist, I'm not sure why...
Your mris_preproc failed or you are not in the directory that has this file. doug
Cheers, Linda
On 3 December 2011 01:26, Douglas N Greve <greve@nmr.mgh.harvard.edu<mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> wrote:
does /home/virtualuser/freesurfer/**subjects/lh.MMSE-AD.thickness.**00.mgh exist? doug
Linda Zhang wrote:
Dear all, I think I figured out the contrasts (I'm using [0 0 0 0 0.5 0.5 0 0]...is that correct?) but I've come across an error when trying to do the next step in the tutorial. I didn't cache the data during recon-all, so I ran the following: mris_preproc --fsgd MMSE-AD.fsgd --target fsaverage --hemi lh --meas thickness --out lh.MMSE-AD.thickness.00.mgh It seemed to run smoothly (I've attached the log below) so I ran the next step: mri_surf2surf --hemi lh --s fsaverage --sval lh.MMSE-AD.thickness.00.mgh --fwhm 10 --cortex --tval lh.MMSE-AD.thickness.10.mgh I got the following error: Reading source surface reg /home/virtualuser/freesurfer/**subjects/fsaverage/surf/lh.**sphere.reg Loading source data mghRead(/home/virtualuser/**freesurfer/subjects/lh.MMSE-** AD.thickness.00.mgh, -1): could not open file ERROR: could not read lh.MMSE-AD.thickness.00.mgh as type 3
Can anyone tell me where the problem is? Thanks! Cheers, Linda The log for mris_preproc (truncated to the last subject and last line): ------------------------------**--------------------- #@# 12/12 avo1249 Fri Dec 2 18:20:04 HKT 2011 -------------- ----------------------- mri_surf2surf --srcsubject avo1249 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.18275/**avo1249.12.mgh --sval /home/virtualuser/freesurfer/**subjects/avo1249/surf/lh.**thickness --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = avo1249 srcval = /home/virtualuser/freesurfer/**subjects/avo1249/surf/lh.** thickness srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.18275/**avo1249.12.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /home/virtualuser/freesurfer/**subjects/avo1249/surf/lh.** sphere.reg Loading source data Reading curvature file /home/virtualuser/freesurfer/**subjects/avo1249/surf/lh.** thickness Reading target surface reg /home/virtualuser/freesurfer/**subjects/fsaverage/surf/lh.** sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842)
surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (121128) Reverse Loop had 15750 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 151248, nTrgMulti = 12594, MnTrgMultiHits = 2.2506 nSrc121 = 78171, nSrcLost = 0, nSrcMulti = 42957, MnSrcMultiHits = 2.36099 Saving target data Saving to ./tmp.mris_preproc.18275/**avo1249.12.mgh ----------------------- mri_concat ./tmp.mris_preproc.18275/**avo0015.1.mgh ./tmp.mris_preproc.18275/**avo0260.2.mgh ./tmp.mris_preproc.18275/**avo0403.3.mgh ./tmp.mris_preproc.18275/**avo0441.4.mgh ./tmp.mris_preproc.18275/**avo0493.5.mgh ./tmp.mris_preproc.18275/**avo0622.6.mgh ./tmp.mris_preproc.18275/**avo0677.7.mgh ./tmp.mris_preproc.18275/**avo0920.8.mgh ./tmp.mris_preproc.18275/**avo1086.9.mgh ./tmp.mris_preproc.18275/**avo1206.10.mgh ./tmp.mris_preproc.18275/**avo1241.11.mgh ./tmp.mris_preproc.18275/**avo1249.12.mgh --o lh.MMSE-AD.thickness.00.mgh On 2 December 2011 11:42, Linda Zhang <lzhang87@gmail.com <mailto:lzhang87@gmail.com> <mailto:lzhang87@gmail.com <mailto:lzhang87@gmail.com>>> wrote: Dear all, I have a bit of an amateur question. I've read the slides and tutorial for group analysis, but I'm still confused about the contrasts. I made my fsgd file, which contains two groups: M and F. I also have three continuous variables: Age, MMSE, Education. I would like to test whether thickness is correlated with MMSE scores, after controlling for gender, age, and education. What should my contrast file be in this case? Thanks for the help! Cheers, Linda ------------------------------**------------------------------**
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422
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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/**compliancelinehttp://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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
In this case you have 4 class variables and 3 continuous, so you'll have 16 regressors (and so 16 elements in your contrast). Your actual contrast vector depends on the order of your class variables in the fsgd. Assuming that the order is MP, FP, MV, FV, then the regressors will have the following meaning: 1. MP-Offset 2. FP-Offset 3. MV-Offset 4. FV-Offset 5-8. Age-Slope 9-12. MMSE-Slope 13-16. Ed-Slope
The contrast you list below would then compute the average thickness of the volunteers, probably not what you want. But I'm not sure what contrast you actually want (not clear from "see if they affect thickness). Can you be more specific/precise? doug
Linda Zhang wrote:
Hi Doug,
Sure, my fsgd file contained two groups originally, M and F. I had three continuous variables, which were Age, MMSE, Education. I wanted to test whether thickness is correlated with MMSE scores after controlling for gender, age and education. I now want to add two more class variables (patient and volunteer), and see if they affect thickness. My question was asking if the contrasts in this case would be [0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0]?
I tried mris_preproc again with a different group, and that worked fine, so maybe it was just a fluke. Thanks!
Cheers, Linda
On 5 December 2011 23:10, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Linda Zhang wrote: Hi Doug, Thanks for the clarification. If I were to add another two class variables (patient and subject, for example) and I wanted to see if they affected thickness, assuming they come after gender in the fsgd file, would the contrasts then be [0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0]? Sorry, I can't remember what your design is (I answer a lot of emails and they often blend together). Can you refresh my memory? From the powerpoint slides, there's an example where two contrast matrices are used (age, gender), what kind of output would that produce? It would produce results (p-values, eg) for each of the contrasts. This allows you to run one command instead of one for each contrast. /home/virtualuser/freesurfer/subjects/lh.MMSE-AD.thickness.00.mgh doesn't exist, I'm not sure why... Your mris_preproc failed or you are not in the directory that has this file. doug Cheers, Linda On 3 December 2011 01:26, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: does /home/virtualuser/freesurfer/subjects/lh.MMSE-AD.thickness.00.mgh exist? doug Linda Zhang wrote: Dear all, I think I figured out the contrasts (I'm using [0 0 0 0 0.5 0.5 0 0]...is that correct?) but I've come across an error when trying to do the next step in the tutorial. I didn't cache the data during recon-all, so I ran the following: mris_preproc --fsgd MMSE-AD.fsgd --target fsaverage --hemi lh --meas thickness --out lh.MMSE-AD.thickness.00.mgh It seemed to run smoothly (I've attached the log below) so I ran the next step: mri_surf2surf --hemi lh --s fsaverage --sval lh.MMSE-AD.thickness.00.mgh --fwhm 10 --cortex --tval lh.MMSE-AD.thickness.10.mgh I got the following error: Reading source surface reg /home/virtualuser/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Loading source data mghRead(/home/virtualuser/freesurfer/subjects/lh.MMSE-AD.thickness.00.mgh, -1): could not open file ERROR: could not read lh.MMSE-AD.thickness.00.mgh as type 3 Can anyone tell me where the problem is? Thanks! Cheers, Linda The log for mris_preproc (truncated to the last subject and last line): --------------------------------------------------- #@# 12/12 avo1249 Fri Dec 2 18:20:04 HKT 2011 -------------- ----------------------- mri_surf2surf --srcsubject avo1249 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.18275/avo1249.12.mgh --sval /home/virtualuser/freesurfer/subjects/avo1249/surf/lh.thickness --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = avo1249 srcval = /home/virtualuser/freesurfer/subjects/avo1249/surf/lh.thickness srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.18275/avo1249.12.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /home/virtualuser/freesurfer/subjects/avo1249/surf/lh.sphere.reg Loading source data Reading curvature file /home/virtualuser/freesurfer/subjects/avo1249/surf/lh.thickness Reading target surface reg /home/virtualuser/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (121128) Reverse Loop had 15750 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 151248, nTrgMulti = 12594, MnTrgMultiHits = 2.2506 nSrc121 = 78171, nSrcLost = 0, nSrcMulti = 42957, MnSrcMultiHits = 2.36099 Saving target data Saving to ./tmp.mris_preproc.18275/avo1249.12.mgh ----------------------- mri_concat ./tmp.mris_preproc.18275/avo0015.1.mgh ./tmp.mris_preproc.18275/avo0260.2.mgh ./tmp.mris_preproc.18275/avo0403.3.mgh ./tmp.mris_preproc.18275/avo0441.4.mgh ./tmp.mris_preproc.18275/avo0493.5.mgh ./tmp.mris_preproc.18275/avo0622.6.mgh ./tmp.mris_preproc.18275/avo0677.7.mgh ./tmp.mris_preproc.18275/avo0920.8.mgh ./tmp.mris_preproc.18275/avo1086.9.mgh ./tmp.mris_preproc.18275/avo1206.10.mgh ./tmp.mris_preproc.18275/avo1241.11.mgh ./tmp.mris_preproc.18275/avo1249.12.mgh --o lh.MMSE-AD.thickness.00.mgh On 2 December 2011 11:42, Linda Zhang <lzhang87@gmail.com <mailto:lzhang87@gmail.com> <mailto:lzhang87@gmail.com <mailto:lzhang87@gmail.com>> <mailto:lzhang87@gmail.com <mailto:lzhang87@gmail.com> <mailto:lzhang87@gmail.com <mailto:lzhang87@gmail.com>>>> wrote: Dear all, I have a bit of an amateur question. I've read the slides and tutorial for group analysis, but I'm still confused about the contrasts. I made my fsgd file, which contains two groups: M and F. I also have three continuous variables: Age, MMSE, Education. I would like to test whether thickness is correlated with MMSE scores, after controlling for gender, age, and education. What should my contrast file be in this case? Thanks for the help! Cheers, Linda ------------------------------------------------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> 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. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Hi Doug,
Our hypothesis is that cortical thickness will be lower in patients than in volunteers, once controlled for gender, age, education, etc. I may remove MMSE as diagnosis of the patient is in part based on the MMSE scores. In that case, I would have 12 regressors, in the order you listed minus the MMSE-slope ones. Should I be using [0 0 -1 1 0 0 0 0 0 0 0 0] or [0 0 1 -1 0 0 0 0 0 0 0 0] to test my hypothesis?
Cheers, Linda
On 7 December 2011 00:01, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
In this case you have 4 class variables and 3 continuous, so you'll have 16 regressors (and so 16 elements in your contrast). Your actual contrast vector depends on the order of your class variables in the fsgd. Assuming that the order is MP, FP, MV, FV, then the regressors will have the following meaning:
- MP-Offset
- FP-Offset
- MV-Offset
- FV-Offset
5-8. Age-Slope 9-12. MMSE-Slope 13-16. Ed-Slope
The contrast you list below would then compute the average thickness of the volunteers, probably not what you want. But I'm not sure what contrast you actually want (not clear from "see if they affect thickness). Can you be more specific/precise? doug
Linda Zhang wrote:
Hi Doug,
Sure, my fsgd file contained two groups originally, M and F. I had three continuous variables, which were Age, MMSE, Education. I wanted to test whether thickness is correlated with MMSE scores after controlling for gender, age and education. I now want to add two more class variables (patient and volunteer), and see if they affect thickness. My question was asking if the contrasts in this case would be [0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0]? I tried mris_preproc again with a different group, and that worked fine, so maybe it was just a fluke. Thanks!
Cheers, Linda
On 5 December 2011 23:10, Douglas N Greve <greve@nmr.mgh.harvard.edu<mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> wrote:
Linda Zhang wrote:
Hi Doug, Thanks for the clarification. If I were to add another two class variables (patient and subject, for example) and I wanted to see if they affected thickness, assuming they come after gender in the fsgd file, would the contrasts then be [0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0]?Sorry, I can't remember what your design is (I answer a lot of emails and they often blend together). Can you refresh my memory?
From the powerpoint slides, there's an example where two contrast matrices are used (age, gender), what kind of output would that produce?It would produce results (p-values, eg) for each of the contrasts. This allows you to run one command instead of one for each contrast.
/home/virtualuser/freesurfer/**subjects/lh.MMSE-AD.thickness.**00.mgh doesn't exist, I'm not sure why...
Your mris_preproc failed or you are not in the directory that has this file. doug
Cheers, Linda On 3 December 2011 01:26, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>>>wrote:
does /home/virtualuser/freesurfer/**subjects/lh.MMSE-AD.thickness.**00.mgh exist? doug
Linda Zhang wrote: Dear all, I think I figured out the contrasts (I'm using [0 0 0 0 0.5 0.5 0 0]...is that correct?) but I've come across an error when trying to do the next step in the tutorial. I didn't cache the data during recon-all, so I ran the following: mris_preproc --fsgd MMSE-AD.fsgd --target fsaverage --hemi lh --meas thickness --out lh.MMSE-AD.thickness.00.mgh It seemed to run smoothly (I've attached the log below) so I ran the next step: mri_surf2surf --hemi lh --s fsaverage --sval lh.MMSE-AD.thickness.00.mgh --fwhm 10 --cortex --tval lh.MMSE-AD.thickness.10.mgh I got the following error: Reading source surface reg /home/virtualuser/freesurfer/**subjects/fsaverage/surf/lh.**sphere.reg Loading source data mghRead(/home/virtualuser/** freesurfer/subjects/lh.MMSE-**AD.thickness.00.mgh, -1): could not open file ERROR: could not read lh.MMSE-AD.thickness.00.mgh as type 3
Can anyone tell me where the problem is? Thanks! Cheers, Linda The log for mris_preproc (truncated to the last subject and last line): ------------------------------**--------------------- #@# 12/12 avo1249 Fri Dec 2 18:20:04 HKT 2011 -------------- ----------------------- mri_surf2surf --srcsubject avo1249 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.18275/**avo1249.12.mgh --sval /home/virtualuser/freesurfer/**subjects/avo1249/surf/lh.**thickness --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = avo1249 srcval = /home/virtualuser/freesurfer/** subjects/avo1249/surf/lh.**thickness srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.18275/**avo1249.12.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /home/virtualuser/freesurfer/** subjects/avo1249/surf/lh.**sphere.reg Loading source data Reading curvature file /home/virtualuser/freesurfer/** subjects/avo1249/surf/lh.**thickness Reading target surface reg /home/virtualuser/freesurfer/** subjects/fsaverage/surf/lh.**sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842)
surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (121128) Reverse Loop had 15750 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 151248, nTrgMulti = 12594, MnTrgMultiHits = 2.2506 nSrc121 = 78171, nSrcLost = 0, nSrcMulti = 42957, MnSrcMultiHits = 2.36099 Saving target data Saving to ./tmp.mris_preproc.18275/**avo1249.12.mgh ----------------------- mri_concat ./tmp.mris_preproc.18275/**avo0015.1.mgh ./tmp.mris_preproc.18275/**avo0260.2.mgh ./tmp.mris_preproc.18275/**avo0403.3.mgh ./tmp.mris_preproc.18275/**avo0441.4.mgh ./tmp.mris_preproc.18275/**avo0493.5.mgh ./tmp.mris_preproc.18275/**avo0622.6.mgh ./tmp.mris_preproc.18275/**avo0677.7.mgh ./tmp.mris_preproc.18275/**avo0920.8.mgh ./tmp.mris_preproc.18275/**avo1086.9.mgh ./tmp.mris_preproc.18275/**avo1206.10.mgh ./tmp.mris_preproc.18275/**avo1241.11.mgh ./tmp.mris_preproc.18275/**avo1249.12.mgh --o lh.MMSE-AD.thickness.00.mgh On 2 December 2011 11:42, Linda Zhang <lzhang87@gmail.com <mailto:lzhang87@gmail.com> <mailto:lzhang87@gmail.com <mailto:lzhang87@gmail.com>> <mailto:lzhang87@gmail.com <mailto:lzhang87@gmail.com> <mailto:lzhang87@gmail.com <mailto:lzhang87@gmail.com>>>> wrote: Dear all, I have a bit of an amateur question. I've read the slides and tutorial for group analysis, but I'm still confused about the contrasts. I made my fsgd file, which contains two groups: M and F. I also have three continuous variables: Age, MMSE, Education. I would like to test whether thickness is correlated with MMSE scores, after controlling for gender, age, and education. What should my contrast file be in this case? Thanks for the help! Cheers, Linda ------------------------------**------------------------------**------------
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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<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.-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Both of those will essentially test the same thing, just with a different sign. FS always computes two-tailed tests and reports both tails, so the sign is only a matter of convention. Assuming the Patient class is first in the FSGD and you want volunteers > patients to show up as yellow, then you would use the first contrast. Note that when you go to correct for multiple comparisons, make sure to specify the sign as "pos" (positive). Also, you should remove the mean from you covariates. doug
Linda Zhang wrote:
Hi Doug,
Our hypothesis is that cortical thickness will be lower in patients than in volunteers, once controlled for gender, age, education, etc. I may remove MMSE as diagnosis of the patient is in part based on the MMSE scores. In that case, I would have 12 regressors, in the order you listed minus the MMSE-slope ones. Should I be using [0 0 -1 1 0 0 0 0 0 0 0 0] or [0 0 1 -1 0 0 0 0 0 0 0 0] to test my hypothesis?
Cheers, Linda
On 7 December 2011 00:01, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
In this case you have 4 class variables and 3 continuous, so you'll have 16 regressors (and so 16 elements in your contrast). Your actual contrast vector depends on the order of your class variables in the fsgd. Assuming that the order is MP, FP, MV, FV, then the regressors will have the following meaning: 1. MP-Offset 2. FP-Offset 3. MV-Offset 4. FV-Offset 5-8. Age-Slope 9-12. MMSE-Slope 13-16. Ed-Slope The contrast you list below would then compute the average thickness of the volunteers, probably not what you want. But I'm not sure what contrast you actually want (not clear from "see if they affect thickness). Can you be more specific/precise? doug Linda Zhang wrote: Hi Doug, Sure, my fsgd file contained two groups originally, M and F. I had three continuous variables, which were Age, MMSE, Education. I wanted to test whether thickness is correlated with MMSE scores after controlling for gender, age and education. I now want to add two more class variables (patient and volunteer), and see if they affect thickness. My question was asking if the contrasts in this case would be [0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0]? I tried mris_preproc again with a different group, and that worked fine, so maybe it was just a fluke. Thanks! Cheers, Linda On 5 December 2011 23:10, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard. edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: Linda Zhang wrote: Hi Doug, Thanks for the clarification. If I were to add another two class variables (patient and subject, for example) and I wanted to see if they affected thickness, assuming they come after gender in the fsgd file, would the contrasts then be [0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0]? Sorry, I can't remember what your design is (I answer a lot of emails and they often blend together). Can you refresh my memory? From the powerpoint slides, there's an example where two contrast matrices are used (age, gender), what kind of output would that produce? It would produce results (p-values, eg) for each of the contrasts. This allows you to run one command instead of one for each contrast. /home/virtualuser/freesurfer/ subjects/lh.MMSE-AD.thickness. 00.mgh doesn't exist, I'm not sure why... Your mris_preproc failed or you are not in the directory that has this file. doug Cheers, Linda On 3 December 2011 01:26, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard. edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard. edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard. edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: does /home/virtualuser/freesurfer/ subjects/lh.MMSE-AD.thickness. 00.mgh exist? doug Linda Zhang wrote: Dear all, I think I figured out the contrasts (I'm using [0 0 0 0 0.5 0.5 0 0]...is that correct?) but I've come across an error when trying to do the next step in the tutorial. I didn't cache the data during recon-all, so I ran the following: mris_preproc --fsgd MMSE-AD.fsgd --target fsaverage --hemi lh --meas thickness --out lh.MMSE-AD.thickness.00.mgh It seemed to run smoothly (I've attached the log below) so I ran the next step: mri_surf2surf --hemi lh --s fsaverage --sval lh.MMSE-AD.thickness.00.mgh --fwhm 10 --cortex --tval lh.MMSE-AD.thickness.10.mgh I got the following error: Reading source surface reg /home/virtualuser/freesurfer/ subjects/fsaverage/surf/lh. sphere.reg Loading source data mghRead(/home/virtualuser/ freesurfer/subjects/lh.MMSE- AD.thickness.00.mgh, -1): could not open file ERROR: could not read lh.MMSE-AD.thickness.00.mgh as type 3 Can anyone tell me where the problem is? Thanks! Cheers, Linda The log for mris_preproc (truncated to the last subject and last line): ------------------------------ --------------------- #@# 12/12 avo1249 Fri Dec 2 18:20:04 HKT 2011 -------------- ----------------------- mri_surf2surf --srcsubject avo1249 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.18275/ avo1249.12.mgh --sval /home/virtualuser/freesurfer/ subjects/avo1249/surf/lh. thickness --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = avo1249 srcval = /home/virtualuser/freesurfer/ subjects/avo1249/surf/lh. thickness srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.18275/ avo1249.12.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /home/virtualuser/freesurfer/ subjects/avo1249/surf/lh. sphere.reg Loading source data Reading curvature file /home/virtualuser/freesurfer/ subjects/avo1249/surf/lh. thickness Reading target surface reg /home/virtualuser/freesurfer/ subjects/fsaverage/surf/lh. sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (121128) Reverse Loop had 15750 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 151248, nTrgMulti = 12594, MnTrgMultiHits = 2.2506 nSrc121 = 78171, nSrcLost = 0, nSrcMulti = 42957, MnSrcMultiHits = 2.36099 Saving target data Saving to ./tmp.mris_preproc.18275/ avo1249.12.mgh ----------------------- mri_concat ./tmp.mris_preproc.18275/ avo0015.1.mgh ./tmp.mris_preproc.18275/ avo0260.2.mgh ./tmp.mris_preproc.18275/ avo0403.3.mgh ./tmp.mris_preproc.18275/ avo0441.4.mgh ./tmp.mris_preproc.18275/ avo0493.5.mgh ./tmp.mris_preproc.18275/ avo0622.6.mgh ./tmp.mris_preproc.18275/ avo0677.7.mgh ./tmp.mris_preproc.18275/ avo0920.8.mgh ./tmp.mris_preproc.18275/ avo1086.9.mgh ./tmp.mris_preproc.18275/ avo1206.10.mgh ./tmp.mris_preproc.18275/ avo1241.11.mgh ./tmp.mris_preproc.18275/ avo1249.12.mgh --o lh.MMSE-AD.thickness.00.mgh On 2 December 2011 11:42, Linda Zhang <lzhang87@gmail.com <mailto:lzhang87@gmail.com> <mailto:lzhang87@gmail.com <mailto:lzhang87@gmail.com>> <mailto:lzhang87@gmail.com <mailto:lzhang87@gmail.com> <mailto:lzhang87@gmail.com <mailto:lzhang87@gmail.com>>> <mailto:lzhang87@gmail.com <mailto:lzhang87@gmail.com> <mailto:lzhang87@gmail.com <mailto:lzhang87@gmail.com>> <mailto:lzhang87@gmail.com <mailto:lzhang87@gmail.com> <mailto:lzhang87@gmail.com <mailto:lzhang87@gmail.com>>>>> wrote: Dear all, I have a bit of an amateur question. I've read the slides and tutorial for group analysis, but I'm still confused about the contrasts. I made my fsgd file, which contains two groups: M and F. I also have three continuous variables: Age, MMSE, Education. I would like to test whether thickness is correlated with MMSE scores, after controlling for gender, age, and education. What should my contrast file be in this case? Thanks for the help! Cheers, Linda ------------------------------ ------------------------------ ------------ ______________________________ _________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh. harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh. harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh. harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard. edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard. edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard. edu <mailto:greve@nmr.mgh.harvard.edu>>> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/ fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh. harvard.edu/fswiki/ BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> <http://surfer.nmr.mgh. harvard.edu/fswiki/ BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> FileDrop: www.nmr.mgh.harvard.edu/ facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard. edu/facility/filedrop/index. html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> <http://www.nmr.mgh.harvard. edu/facility/filedrop/index. html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> 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 <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. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard. edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/ fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh. harvard.edu/fswiki/ BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> FileDrop: www.nmr.mgh.harvard.edu/ facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard. edu/facility/filedrop/index. html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/ fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/ facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Linda Zhang