Can I use data processed by other tool like FSL, or I can only use DTI
image after Freesurfer processing?

On Fri, Nov 10, 2017 at 3:07 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
wrote:

> Yes
>
> On 11/10/17 2:45 PM, lanbo Wang wrote:
>
> Thank you very much, it's work.
> I have another question, this is for structural imaging. Can I use those
> steps for fmri or DTI imaging?
>
> On Fri, Nov 10, 2017 at 1:08 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
> wrote:
>
>> Don't use --conjunct, just mri_concat file1 file2 ... file N --o output
>>
>> On 11/10/17 12:56 PM, lanbo Wang wrote:
>>
>> I firstly did mris_preproc separately. Secondly used fscalc to reverse
>> left symptom subjects. Thirdly used mri_concat --conjunct to combine all
>> the subjects together.
>>
>> The code is:
>> 1.mris_preproc --target fsaverage_sym --hemi lh \
>>   --xhemi --paired-diff \
>>   --srcsurfreg fsaverage_sym.sphere.reg \
>>   --meas thickness \
>>   --out lh.lh-rh.thickness.sm00.s02.mgh \
>>   --s subj_02_1
>> 2. fscalc lh.lh-rh.thickness.sm00.s09.mgh mul -1 -o
>> lh.lh-rh.thickness.sm00.s09.mgh
>> 3.mri_concat --conjunct --i lh.lh-rh.thickness.sm00.s02.mgh
>> lh.lh-rh.thickness.sm00.s03.mgh lh.lh-rh.thickness.sm00.s04.mgh
>> lh.lh-rh.thickness.sm00.s05.mgh lh.lh-rh.thickness.sm00.s06.mgh
>> lh.lh-rh.thickness.sm00.s08.mgh lh.lh-rh.thickness.sm00.s09.mgh
>> lh.lh-rh.thickness.sm00.s10.mgh lh.lh-rh.thickness.sm00.s11.mgh
>> lh.lh-rh.thickness.sm00.s12.mgh lh.lh-rh.thickness.sm00.s13.mgh
>> lh.lh-rh.thickness.sm00.s14.mgh lh.lh-rh.thickness.sm00.s15.mgh
>> lh.lh-rh.thickness.sm00.s16.mgh lh.lh-rh.thickness.sm00.s17.mgh
>> lh.lh-rh.thickness.sm00.s18.mgh lh.lh-rh.thickness.sm00.s19.mgh
>> lh.lh-rh.thickness.sm00.s20.mgh lh.lh-rh.thickness.sm00.s21.mgh
>> lh.lh-rh.thickness.sm00.s22.mgh lh.lh-rh.thickness.sm00.s24.mgh
>> lh.lh-rh.thickness.sm00.s25.mgh lh.lh-rh.thickness.sm00.s26.mgh
>> lh.lh-rh.thickness.sm00.s27.mgh lh.lh-rh.thickness.sm00.s29.mgh
>> lh.lh-rh.thickness.sm00.s32.mgh --o lh.lh-rh.thickness.sm00.mgh
>> 4.smooth
>> 5.mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir
>> glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh
>>
>>
>> On Fri, Nov 10, 2017 at 11:17 AM, Douglas Greve <
>> gr...@nmr.mgh.harvard.edu> wrote:
>>
>>> Do you only have one subject in your input file? You need to run
>>> mris_preproc separately for each subject, create a different file for each,
>>> then mri_concat the files together
>>>
>>> On 11/9/17 6:20 PM, lanbo Wang wrote:
>>>
>>> Dr. Douglas,
>>>
>>> I try #3 method, when I run mri_glmfit, get error.
>>> The code I used:
>>> [mtobia@localhost lh.lh-rh.thickness]$ mri_glmfit --y
>>> lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm
>>> --surf fsaverage_sym lh
>>> Reading source surface /HD4/subjects_results_symptom/
>>> /fsaverage_sym/surf/lh.white
>>> Number of vertices 163842
>>> Number of faces    327680
>>> Total area         61972.710938
>>> AvgVtxArea       0.378247
>>> AvgVtxDist       0.693419
>>> StdVtxDist       0.190498
>>>
>>> $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
>>> cwd /HD4/subjects_results_symptom/lh.lh-rh.thickness
>>> cmdline mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir
>>> glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh
>>> sysname  Linux
>>> hostname localhost.localdomain
>>> machine  x86_64
>>> user     mtobia
>>> FixVertexAreaFlag = 1
>>> UseMaskWithSmoothing     1
>>> OneSampleGroupMean 1
>>> y    /HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.th
>>> ickness.sm10.mgh
>>> logyflag 0
>>> usedti  0
>>> labelmask  /HD4/subjects_results_symptom//fsaverage_sym/label/lh.cortex
>>> .label
>>> maskinv 0
>>> glmdir glm.lh.lh-rh.thickness.sm10
>>> IllCondOK 0
>>> ReScaleX 1
>>> DoFFx 0
>>> Creating output directory glm.lh.lh-rh.thickness.sm10
>>> Loading y from /HD4/subjects_results_symptom/lh.lh-rh.thickness/
>>> lh.lh-rh.thickness.sm10.mgh
>>> Saving design matrix to glm.lh.lh-rh.thickness.sm10/Xg.dat
>>> Normalized matrix condition is 1
>>> Matrix condition is 1
>>> Found 146902 points in label.
>>> Pruning voxels by thr: 0.000000
>>> Found 146902 voxels in mask
>>> Saving mask to glm.lh.lh-rh.thickness.sm10/mask.mgh
>>> Reshaping mriglm->mask...
>>> search space = 79288.081914
>>> DOF = 0
>>> ERROR: DOF = 0
>>>
>>> The code I used before this one is
>>> How can I resolve this problem.
>>>
>>> Thanks,
>>> Lanbo
>>>
>>>
>>> On Tue, Nov 7, 2017 at 6:10 PM, Douglas N Greve <
>>> gr...@nmr.mgh.harvard.edu> wrote:
>>>
>>>> which code. I gave 3 options below, which one did you use?
>>>>
>>>>
>>>> On 11/07/2017 02:43 PM, lanbo Wang wrote:
>>>> > I try to use this code to compare left and right hemisphere by paired
>>>> > t-test  and add age as covariate.
>>>> >
>>>> > Thanks,
>>>> > Lanbo
>>>> >
>>>> > On Tue, Nov 7, 2017 at 11:40 AM, Douglas N Greve
>>>> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>>> >
>>>> >     which method are you trying to implement? If #3, then you need to
>>>> run
>>>> >     mris_preproc separately for each subject, and then run that fscalc
>>>> >     command
>>>> >
>>>> >
>>>> >     On 11/07/2017 11:33 AM, lanbo Wang wrote:
>>>> >     > Hi Douglas,
>>>> >     >
>>>> >     > Thanks for your reply.
>>>> >     > I created the fsgd file as you show me, and run code like this.
>>>> Am I
>>>> >     > right?
>>>> >     > 1.
>>>> >     > mris_preproc --fsgd Subject.xhemi.dat \
>>>> >     >   --target fsaverage_sym --hemi lh \
>>>> >     >   --xhemi --paired-diff \
>>>> >     >   --srcsurfreg fsaverage_sym.sphere.reg \
>>>> >     >   --meas thickness \
>>>> >     >   --out lh.lh-rh.thickness.age.sm00.mgh \
>>>> >     >  --s subj_02_1  --s subj_04_1  --s subj_05_1  --s subj_06_1  --s
>>>> >     > subj_08_1  --s subj_09_1  --s subj_10_1 --s subj_11_1  --s
>>>> >     subj_12_1
>>>> >     > --s subj_13_1  --s subj_14_1  --s subj_15_1  --s subj_16_1  --s
>>>> >     > subj_17_1 --s subj_18_1  --s subj_20_1  --s subj_21_1  --s
>>>> >     subj_22_1
>>>> >     > --s subj_24_1  --s subj_25_1  --s subj_26_1 --s subj_27_1  --s
>>>> >     > subj_29_1  --s subj_32_1
>>>> >     >
>>>> >     > 2.
>>>> >     > mri_glmfit --y lh.lh-rh.thickness.age.sm10.mgh --glmdir
>>>> >     > glm.lh.lh-rh.thickness.age.sm10 \
>>>> >     > --fsgd Subject.xhemi.dat \
>>>> >     > --C Avg-thickness-age-Cor.mtx \
>>>> >     > --surf fsaverage_sym lh
>>>> >     >
>>>> >     > Attachment is fsgd and Avg-thickness-age-cor.mtx.
>>>> >     >
>>>> >     > All best,
>>>> >     > Lanbo Wang
>>>> >     >
>>>> >     >
>>>> >     > On Tue, Nov 7, 2017 at 10:18 AM, Bruce Fischl
>>>> >     > <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>
>>>> >     <mailto:fis...@nmr.mgh.harvard.edu
>>>> >     <mailto:fis...@nmr.mgh.harvard.edu>>> wrote:
>>>> >     >
>>>> >     >     Hi Danny
>>>> >     >
>>>> >     >     you need to give us more information if you want us to help
>>>> you.
>>>> >     >     Please include the command you ran and the entire screen
>>>> output.
>>>> >     >
>>>> >     >     cheers
>>>> >     >     Bruce
>>>> >     >
>>>> >     >
>>>> >     >     On Tue, 7 Nov 2017, Danny Deng wrote:
>>>> >     >
>>>> >     >         Dear FDs,
>>>> >     >         I encountered an odd situation:
>>>> >     >
>>>> >     >         My free surfer will always shut down when I run command.
>>>> >     >
>>>> >     >         My MacOS version is 10.12.6 (16G29) processor: 1.6 GHz
>>>> Intel
>>>> >     >         Core i5
>>>> >     >
>>>> >     >         I don’t know if the compatibility is fine with my
>>>> download
>>>> >     >         version (MacOS Lion OS X 10.7 (64b
>>>> >     >         intel)Stable v6.0.0)
>>>> >     >
>>>> >     >         Please kindly suggest.
>>>> >     >
>>>> >     >         Thanks ver much
>>>> >     >
>>>> >     >         Best Regards,Danny Deng
>>>> >     >
>>>> >     >
>>>> >     >               On Nov 7, 2017, at 7:14 AM, Douglas N Greve
>>>> >     >         <gr...@nmr.mgh.harvard.edu
>>>> >     <mailto:gr...@nmr.mgh.harvard.edu>
>>>> >     <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.
>>>> edu>>>
>>>> >     >         wrote:
>>>> >     >
>>>> >     >
>>>> >     >
>>>> >     >         On 11/06/2017 12:03 PM, lanbo Wang wrote:
>>>> >     >               Dear experts,
>>>> >     >
>>>> >     >               I have two questions about hemisphere analysis:
>>>> >     >
>>>> >     >               1) When I run left-right hemisphere paired t-test,
>>>> >     can I
>>>> >     >         add age as
>>>> >     >               covariate? If use fsgd to add covariate, to this
>>>> >     paired
>>>> >     >         t-test
>>>> >     >               analysis, how to make the fsgd table?
>>>> >     >
>>>> >     >         use this one-group, one-covariate example
>>>> >     > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V
>>>> >     <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V>
>>>> >     >         <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V
>>>> >     <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V>>
>>>> >     >               2) I want to reorganize the hemisphere from
>>>> >     left-right to
>>>> >     >               symptom-nosymptom according to body symptom side
>>>> >     record
>>>> >     >         and compare
>>>> >     >               different between symptom hemisphere and nosymptom
>>>> >     >         hemisphere. Can I
>>>> >     >               use freesurfer to do it?
>>>> >     >
>>>> >     >         Yes, though it is a little tricky with multiple ways,
>>>> each
>>>> >     >         complicated
>>>> >     >         in its own way.
>>>> >     >         1. Create your own design matrix. You can use the one
>>>> >     created by
>>>> >     >         mri_glmfit to start. Assuming you want
>>>> >     >         symptomHemi-nosymptomHemi, then,
>>>> >     >         in each subject whose symptomHemi is rh, multiply its
>>>> >     line in
>>>> >     >         the design
>>>> >     >         matrix by -1. Then pass this design matrix to mri_glmfit
>>>> >     with --X
>>>> >     >         instead of passing an FSGD file.
>>>> >     >         2. Load the output of mris_preproc into matlab, eg, y =
>>>> >     >         MRIread('y.mgh');, then change the sign as in #1 above,
>>>> eg,
>>>> >     >         y.vol(:,:,:,10) = -y.vol(:,:,:,10); and so on for each
>>>> >     applicable
>>>> >     >         subject. Then save the data with
>>>> MRIwrite(y,'new.y.mgh');,
>>>> >     >         then run
>>>> >     >         mri_glmfit as normal with the new file.
>>>> >     >         3. Run mris_preproc for each subject separately to
>>>> >     generate an
>>>> >     >         lh.lh-rh.thickness.sm00.subject10.mgh file. Then
>>>> change the
>>>> >     >         sign as in
>>>> >     >         #1 above with
>>>> >     >         fscalc lh.lh-rh.thickness.sm00.subject10.mgh mul -1 -o
>>>> >     >         lh.lh-rh.thickness.sm00.subject10.mgh
>>>> >     >         Then run mri_concat to concatenate all the subjects
>>>> together
>>>> >     >         in the same
>>>> >     >         order as they are listed in the FSGD file, then use this
>>>> >     stack
>>>> >     >         as input
>>>> >     >         the mri_glmfit
>>>> >     >
>>>> >     >
>>>> >     >               Thanks for your patient and help.
>>>> >     >
>>>> >     >               All best,
>>>> >     >               Lanbo Wang
>>>> >     >
>>>> >     >
>>>> >     >               _______________________________________________
>>>> >     >               Freesurfer mailing list
>>>> >     > Freesurfer@nmr.mgh.harvard.edu
>>>> >     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>> >     >         <mailto:Freesurfer@nmr.mgh.harvard.edu
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>>>> >     >
>>>> >     >
>>>> >     >         --
>>>> >     >         Douglas N. Greve, Ph.D.
>>>> >     >         MGH-NMR Center
>>>> >     > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>>>> >     <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.
>>>> edu>>
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>>>> >     <tel:617-724-2358 <tel:617-724-2358>>
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>>>> >     <tel:617-726-7422>>
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>>>> >     >
>>>> >     >         _______________________________________________
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>>>> >     --
>>>> >     Douglas N. Greve, Ph.D.
>>>> >     MGH-NMR Center
>>>> >     gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>>>> >     Phone Number: 617-724-2358 <tel:617-724-2358>
>>>> >     Fax: 617-726-7422 <tel:617-726-7422>
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>>>> --
>>>> Douglas N. Greve, Ph.D.
>>>> MGH-NMR Center
>>>> gr...@nmr.mgh.harvard.edu
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>>
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>> 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.
>>
>>
>
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> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
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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 . 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.

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