[Freesurfer] QDEC

[Kinzel, Phillipp]

Hi, I have problems loading project  files in QDEC.

I get the following error:

Loading data table /tmp/qdec_project_archive/qdec.table.dat...
ERROR: could not open /tmp/qdec_project_archive/qdec.table.dat
Error loading the project file.

I would be greatful for any advice.

Best, Philipp


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Re: [Freesurfer] problems of testing freesurfer

[Hoopes, Andrew]

Hi Danny,

The SUBJECTS_DIR variable defines the path to a directory where freesurfer 
recon data is stored for a particular study. When setting this path variable, 
you don’t need to include the <> brackets.

After sourcing freesurfer, start by making a sample directory and defining your 
SUBJECTS_DIR like this:
mkdir test_subjects
export SUBJECTS_DIR=/path/to/test_subjects

then try running a sample recon:
cd ${FREESURFER_HOME}/subjects
recon-all -i sample-001.nii.gz -s bert -all

best,
Andrew

On Nov 7, 2017, at 7:19 PM, Danny Deng 
> wrote:

Hi developers,

I just installed the software and there are so many problems I wish to seek 
help from you when I tried “Test your freesurfer installation” on the website

Example 2

I tried several commands as follow but all failed:

1. Xues-MacBook-Air:~ DannyDeng$ export 
SUBJECTS_DIR=<$FREESURFER_HOME/subjects/sample-001.mgz .>
-bash: syntax error near unexpected token `newline’

2. Xues-MacBook-Air:~ DannyDeng$ > export SUBJECTS_DIR=
-bash: syntax error near unexpected token `newline’

3. Xues-MacBook-Air:~ DannyDeng$ >export 
SUBJECTS_DIR=<_HOME/subjects/sample-001.mgz .>
-bash: syntax error near unexpected token `newline’

4. DannyDeng$ DannyDeng$SUBJECTS_DIR
-bash: DannyDengcp/Applications/freesurfer/subjects/sample-001.mgz: No such 
file or directory

Besides, I think I can’t find nifti file in my freesurfer folder.

example 3

Same problem like example 2:

Xues-MacBook-Air:~ DannyDeng$ export SUBJECTS_DIR=
-bash: syntax error near unexpected token `newline’

example 4: Only this one I successfully opened it.

Thanks very much.

Best Regards,
Danny Deng

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[Freesurfer] problems of testing freesurfer

[Danny Deng]

Hi developers,

I just installed the software and there are so many problems I wish to seek 
help from you when I tried “Test your freesurfer installation” on the website

Example 2

I tried several commands as follow but all failed:

1. Xues-MacBook-Air:~ DannyDeng$ export 
SUBJECTS_DIR=<$FREESURFER_HOME/subjects/sample-001.mgz .>
-bash: syntax error near unexpected token `newline’

2. Xues-MacBook-Air:~ DannyDeng$ > export SUBJECTS_DIR=
-bash: syntax error near unexpected token `newline’

3. Xues-MacBook-Air:~ DannyDeng$ >export 
SUBJECTS_DIR=<_HOME/subjects/sample-001.mgz .>
-bash: syntax error near unexpected token `newline’

4. DannyDeng$ DannyDeng$SUBJECTS_DIR
-bash: DannyDengcp/Applications/freesurfer/subjects/sample-001.mgz: No such 
file or directory

Besides, I think I can’t find nifti file in my freesurfer folder.

example 3

Same problem like example 2:

Xues-MacBook-Air:~ DannyDeng$ export SUBJECTS_DIR=
-bash: syntax error near unexpected token `newline’

example 4: Only this one I successfully opened it.

Thanks very much.

Best Regards,
Danny Deng

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Re: [Freesurfer] hemisphere analysis

[Douglas N Greve]

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 
> > 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
> > 
>  >> 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
> >          
> >>
> >         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
> 
> >          >
> >               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 

[Freesurfer] Compare longitudinal evolution of two vertex-wise data

[Matthieu Vanhoutte]

Dear experts,

Do you know if there would be a mean to compare longitudinal evolution of
two vertex-wise data (i.e. kind of longitudinal correlation) with LME tools
or others ?

Best regards,
Matthieu
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Re: [Freesurfer] hemisphere analysis

[lanbo Wang]

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 
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
> > > 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
> > >
> > 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
> > 
> >   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
> >
> >
> >   

Re: [Freesurfer] Local gyrification index - vertex-wise analysis values

[Douglas N Greve]

Intensity Mean will be the mean value of the input (lGI) averaged over 
the ROI.

STD, Max, Min, and Range are the intensity stddev maximimum mininum 
andrange=max-min over the ROI


On 11/07/2017 12:57 PM, Buse Merve Ürgen wrote:
> Dear Freesurfers,
>
> I have two questions:
>
> 1) In the last stage of the recon-all -s  -localGI analysis, 
> local gyrification index values are calculated at each pial vertices. 
> Is there any way (command?) to extract /vertex-wise local gyrification 
> index values/ (of individual subjects) /before running GLM analysis in 
> Qdec/? GLM analysis is not suitable for my study (single-case), so I 
> need to extract values for each subject and use them for my own 
> statistical analysis.
>
> 2) As far as I know we can extract /parcel-wise lGI/ values using the 
> following command:
>
> mri_segstats --annot /subjID/ lh aparc \
>
>   --i $SUBJECTS_DIR//subjID//surf/lh.pial_lgi \
>
>   --sum lh.aparc.pial_lgi.stats
>
>
> Running this command provides "Intensity Mean, Intensity STD, 
> Intensity Max, Intensity Min, Intensity Range" values for each 
> parcellated area. Can you explain these values and what they mean?
>
>
> Thanks,
>
> -Buse
>
>
>
>
> On 5 November 2017 at 19:54, Buse Merve Ürgen  > wrote:
>
> Dear Freesurfer developers,
>
> I would like to run Local Gyrification Index analysis for a group
> of healthy controls and a single patient. After running recon-all
> -s  -localGI command, we get lh.pial_lgi and rh.pial_lgi
> surf files. In the last stage of this analysis, local gyrification
> index values are calculated at each pial vertices.
>
> In the wiki, it is said that the next process should be done in
> qdec, but since I have only one patient, GLM analysis would not be
> suitable. Thus, I would like to get the LGI values of each subject
> as e.g. text files (like stats files for curvature, thickness, gm
> volume), and use them for my own analysis (not in qdec). I know
> that we can get parcel-wise anaysis values using this command:
> mri_segstats --annot CASE lh aparc \
>
>   --i $SUBJECTS_DIR/CASE/surf/lh.pial_lgi \
>
>   --sum lh.aparc.pial_lgi.stats
>
> But I would like to use vertex-wise analysis values for my won
> analysis. Is it possible? Can I learn the command I need to use to
> get these values for each subject?
>
> Thank you,
> Buse
>
> -- 
>
> Buse
>
> ​ Urgen
>
>
>
>
> -- 
>
> Buse M. Ürgen
>
> Ph.D. Candidate Neuroscience Graduate Program National Magnetic 
> Resonance Research Center (UMRAM) & Aysel Sabuncu Brain Research 
> Center Bilkent University Ankara, 06800 Turkey
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Local gyrification index - vertex-wise analysis values

[Buse Merve Ürgen]

Dear Freesurfers,

I have two questions:

1) In the last stage of the recon-all -s  -localGI analysis, local
gyrification index values are calculated at each pial vertices. Is there
any way (command?) to extract *vertex-wise local gyrification index values*
(of individual subjects) *before running GLM analysis in Qdec*? GLM
analysis is not suitable for my study (single-case), so I need to extract
values for each subject and use them for my own statistical analysis.

2) As far as I know we can extract *parcel-wise lGI* values using the
following command:

mri_segstats --annot *subjID* lh aparc \

  --i $SUBJECTS_DIR/*subjID*/surf/lh.pial_lgi \

  --sum lh.aparc.pial_lgi.stats


Running this command provides "Intensity Mean, Intensity STD, Intensity
Max, Intensity Min, Intensity Range" values for each parcellated area. Can
you explain these values and what they mean?


Thanks,

-Buse



On 5 November 2017 at 19:54, Buse Merve Ürgen  wrote:

> Dear Freesurfer developers,
>
> I would like to run Local Gyrification Index analysis for a group of
> healthy controls and a single patient. After running  recon-all -s 
> -localGI  command, we get lh.pial_lgi and rh.pial_lgi surf files. In the
> last stage of this analysis, local gyrification index values are calculated
> at each pial vertices.
>
> In the wiki, it is said that the next process should be done in qdec, but
> since I have only one patient, GLM analysis would not be suitable. Thus, I
> would like to get the LGI values of each subject as e.g. text files (like
> stats files for curvature, thickness, gm volume), and use them for my own
> analysis (not in qdec). I know that we can get parcel-wise anaysis values
> using this command:
> mri_segstats --annot CASE lh aparc \
>
>   --i $SUBJECTS_DIR/CASE/surf/lh.pial_lgi \
>
>   --sum lh.aparc.pial_lgi.stats
>
> But I would like to use vertex-wise analysis values for my won analysis.
> Is it possible? Can I learn the command I need to use to get these values
> for each subject?
>
> Thank you,
> Buse
>
> --
>
> Buse
> ​ Urgen
>
>


-- 

Buse M. Ürgen


Ph.D. Candidate
Neuroscience Graduate Program
National Magnetic Resonance Research Center (UMRAM) &
Aysel Sabuncu Brain Research Center

Bilkent University
Ankara, 06800
Turkey
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Re: [Freesurfer] Qdec result

[Douglas N Greve]

They might be very similar if there is not effect of genotype or the 
effect is orthogonal to age.


On 10/30/2017 03:39 AM, hiroki.s...@med.tohoku.ac.jp wrote:
> Dear experts
>
> I'm using Qdec.
> I want to check regions where age and thickness are correlated, and
> regions where the thickness-age correlation differ between
> genotype(Hetero or WT).
>
> When I choose "genotype(Hetero or WT)" as Fixed factors and "age" as
> Continuous variables, I can choice the results
> "Does the correlation between thickness and age, accounding for
> genotype, differ from zero"
>and
> "Does the thickness-age correlation differ between Hetero and WT?".
>
> I have two questions.
>
> Is "Does the correlation between thickness and age, accounding for
> genotype, differ from zero" equal to the results of "Does the
> correlation between thickness and age differ from zero" that I choose
> only "age" as Continuous variables?
> I don't know the meaning of "accounding for genotype" but these two
> results are almost same. Does just a little different results come from
> the difference of Degrees Of Freedom?
>
> Thank you in advance.
>
> Best,
> Hiroki
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] missing register.dof6.dat

[Douglas N Greve]

There should be an lta file there. Are you getting an error somewhere?


On 10/30/2017 10:54 AM, Guy Avraham wrote:
> ​Hello Freesurfer developers,
>
> I was running FSFAST preprocessing​:
>
> preproc-sess -s
> ​[subject]
> -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 0 -per-run
>
> ​The process finished without errors. However, the ​register.dof6.dat 
> is missing from the subject's folder. I could not find any error in 
> the ​register.dof6.dat.log file (see attached).
>
> - Freesurfer version: 
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> - OS: Ubuntu 16.04 LTS
> - recon-all.log file is also attached.
>
> Thanks!
> Guy
>
>
>
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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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
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] cut-off clusters size

[Douglas N Greve]

There is not, that is not the way that FDR is used


On 11/01/2017 11:35 AM, std...@virgilio.it wrote:
> Hi,
>
> I wonder if there is a consensus to thershold the size of clusters 
> obtained by FS-FAST after FDR correction?
> To cut-off clusters size>10-15 mm2 should be good? or do you advise 
> more than?
>
> Thanks
> Stefano
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] hemisphere analysis

[Douglas N Greve]

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 
> > 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
> >
> 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
> 
>       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
> 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 

Re: [Freesurfer] hemisphere analysis

[lanbo Wang]

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 
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> 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
>>   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
>>   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> 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
> 

Re: [Freesurfer] surface based fMRI gorup analysis from spm

[Douglas N Greve]

looks like you did not create the lta file properly. You can just pass 
mris_preproc the .dat file instead of the lta.


On 11/07/2017 10:51 AM, Elisa Castaldi wrote:
> Yes, the output is in native functional space.
>
> On 7 November 2017 at 16:40, Douglas N Greve 
> > wrote:
>
> Did you keep the spm output in native functional space?
>
>
> On 11/07/2017 09:23 AM, Elisa Castaldi wrote:
> > Yes,
> > this is what I have already done: I moved both the fsaverage and the
> > subjects into SUBJECTS_DIR and the error I get is ERROR: source
> volume
> > is neither source nor target of the registration.
> >
> > On 7 November 2017 at 15:11, Douglas Greve
> 
> >  >> wrote:
> >
> >     When you look in SUBJECTS_DIR,  you should see fsaverage and all
> >     the subjects being passed to mris_preproc. If not, you need to
> >     move them (or sym link them) into that folder.
> >
> >
> >     On 11/7/17 6:07 AM, Elisa Castaldi wrote:
> >>     Thanks for your answer.
> >>     If I don't specify the directory I get the following error
> >>     ERROR: cannot find fsaverage in SUBJECTS_DIR
> >>
> >>     and if I move fsaverage to SUBJECTS_DIR it says that it cannot
> >>     find manat_mp1 which is the name of the folder containing the
> >>     results of recon all for the subject sub01 (contained in the
> >>     SUBJECTS_DIR/surfaces folder). If then I move the manat_mp1
> >>     folder into SUBJECTS_DIR it starts running, but then gives the
> >>     following error ERROR: source volume is neither source nor
> target
> >>     of the registration.
> >>     Below the entire list of output printed before the error
> >>
> >>     mris_preproc --out lh.con.mgh --target fsaverage --hemi lh \
> >>     > --iv ${SUBJECTS_DIR}/sub01/stats/con_0001.nii
> >>     ${SUBJECTS_DIR}/sub01/fmri/mp1reg.lta\
> >>     nsubjects = 1
> >>     tmpdir is ./tmp.mris_preproc.30824
> >>     SUBJECTS_DIR
> >>     Log file is lh.con.mris_preproc.log
> >>
> >>     setenv SUBJECTS_DIR
> >>     cd /SUBJECTS_DIR
> >>     /i2bm/local/freesurfer/bin/mris_preproc --out lh.con.mgh
> --target
> >>     fsaverage --hemi lh --iv /SUBJECTS_DIR/sub01/stats/con_0001.nii
> >>     /SUBJECTS_DIR/sub01/fmri/mp1reg.lta
> >>
> >>     $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $
> >>     freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> >>     tmpdir is ./tmp.mris_preproc.30824
> >>     Src lh sphere.reg
> >>     Trg lh sphere.reg
> >>
> >>     ---
> >>     #@# 1/1 manat_mp1  --
> >>     ---
> >>     mri_vol2surf --src /SUBJECTS_DIR/sub01/stats/con_0001.nii
> >>     --srcreg /SUBJECTS_DIR/sub01/fmri/mp1reg.lta --hemi lh --out
> >>     ./tmp.mris_preproc.30824/subjsurfvals.mgh --cortex --noreshape
> >>     srcvol = SUBJECTS_DIR/sub01/stats/con_0001.nii
> >>     srcreg = /SUBJECTS_DIR/sub01/fmri/mp1reg.lta
> >>     srcregold = 0
> >>     srcwarp unspecified
> >>     surf = white
> >>     hemi = lh
> >>     reshape = 0
> >>     interp = nearest
> >>     float2int = round
> >>     GetProjMax = 0
> >>     INFO: float2int code = 0
> >>     Done loading volume
> >>     Input reg is LTA
> >>
> >>     type  = 0 # LINEAR_VOX_TO_VOX
> >>     nxforms   = 1
> >>     mean  = 0. 0. 0.
> >>     sigma = 1.
> >>     1 4 4
> >>     9.66621398926e-01 2.551120938733220e-03
> 5.084594013169408e-04
> >>     -5.48828125000e-01
> >>     4.461563366930932e-04 2.438484877347946e-02
> >>     -9.997024536132812e-01 2.180384216308594e+02
> >>     -2.562706125900149e-03 9.996992945671082e-01
> >>     2.438353188335896e-02 -5.147048950195312e+00
> >>     0.000e+00 0.000e+00
> 0.000e+00
> >>     1.000e+00
> >>     src volume info
> >>     valid = 1  # volume info valid
> >>     filename = /SUBJECTS_DIR/sub01/fmri/bbrumeanSBref_sess1_mp1.nii
> >>     volume = 256 256 256
> >>     voxelsize = 1.000e+00 1.000e+00
> >>     1.000e+00
> >>     xras   = -1.000e+00 0.000e+00
> >>     0.000e+00
> >>     yras   = 0.000e+00 0.000e+00
> >>     -1.000e+00
> >>     zras   = 0.000e+00 1.000e+00
> >>     0.000e+00
> >>     cras   = 1.867614746093750e+00 -1.400651550292969e+01
> >>     

Re: [Freesurfer] surface based fMRI gorup analysis from spm

[Elisa Castaldi]

Yes, the output is in native functional space.

On 7 November 2017 at 16:40, Douglas N Greve 
wrote:

> Did you keep the spm output in native functional space?
>
>
> On 11/07/2017 09:23 AM, Elisa Castaldi wrote:
> > Yes,
> > this is what I have already done: I moved both the fsaverage and the
> > subjects into SUBJECTS_DIR and the error I get is ERROR: source volume
> > is neither source nor target of the registration.
> >
> > On 7 November 2017 at 15:11, Douglas Greve  > > wrote:
> >
> > When you look in SUBJECTS_DIR,  you should see fsaverage and all
> > the subjects being passed to mris_preproc. If not, you need to
> > move them (or sym link them) into that folder.
> >
> >
> > On 11/7/17 6:07 AM, Elisa Castaldi wrote:
> >> Thanks for your answer.
> >> If I don't specify the directory I get the following error
> >> ERROR: cannot find fsaverage in SUBJECTS_DIR
> >>
> >> and if I move fsaverage to SUBJECTS_DIR it says that it cannot
> >> find manat_mp1 which is the name of the folder containing the
> >> results of recon all for the subject sub01 (contained in the
> >> SUBJECTS_DIR/surfaces folder). If then I move the manat_mp1
> >> folder into SUBJECTS_DIR it starts running, but then gives the
> >> following error ERROR: source volume is neither source nor target
> >> of the registration.
> >> Below the entire list of output printed before the error
> >>
> >> mris_preproc --out lh.con.mgh --target fsaverage --hemi lh \
> >> > --iv ${SUBJECTS_DIR}/sub01/stats/con_0001.nii
> >> ${SUBJECTS_DIR}/sub01/fmri/mp1reg.lta\
> >> nsubjects = 1
> >> tmpdir is ./tmp.mris_preproc.30824
> >> SUBJECTS_DIR
> >> Log file is lh.con.mris_preproc.log
> >>
> >> setenv SUBJECTS_DIR
> >> cd /SUBJECTS_DIR
> >> /i2bm/local/freesurfer/bin/mris_preproc --out lh.con.mgh --target
> >> fsaverage --hemi lh --iv /SUBJECTS_DIR/sub01/stats/con_0001.nii
> >> /SUBJECTS_DIR/sub01/fmri/mp1reg.lta
> >>
> >> $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $
> >> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> >> tmpdir is ./tmp.mris_preproc.30824
> >> Src lh sphere.reg
> >> Trg lh sphere.reg
> >>
> >> ---
> >> #@# 1/1 manat_mp1  --
> >> ---
> >> mri_vol2surf --src /SUBJECTS_DIR/sub01/stats/con_0001.nii
> >> --srcreg /SUBJECTS_DIR/sub01/fmri/mp1reg.lta --hemi lh --out
> >> ./tmp.mris_preproc.30824/subjsurfvals.mgh --cortex --noreshape
> >> srcvol = SUBJECTS_DIR/sub01/stats/con_0001.nii
> >> srcreg = /SUBJECTS_DIR/sub01/fmri/mp1reg.lta
> >> srcregold = 0
> >> srcwarp unspecified
> >> surf = white
> >> hemi = lh
> >> reshape = 0
> >> interp = nearest
> >> float2int = round
> >> GetProjMax = 0
> >> INFO: float2int code = 0
> >> Done loading volume
> >> Input reg is LTA
> >>
> >> type  = 0 # LINEAR_VOX_TO_VOX
> >> nxforms   = 1
> >> mean  = 0. 0. 0.
> >> sigma = 1.
> >> 1 4 4
> >> 9.66621398926e-01 2.551120938733220e-03 5.084594013169408e-04
> >> -5.48828125000e-01
> >> 4.461563366930932e-04 2.438484877347946e-02
> >> -9.997024536132812e-01 2.180384216308594e+02
> >> -2.562706125900149e-03 9.996992945671082e-01
> >> 2.438353188335896e-02 -5.147048950195312e+00
> >> 0.000e+00 0.000e+00 0.000e+00
> >> 1.000e+00
> >> src volume info
> >> valid = 1  # volume info valid
> >> filename = /SUBJECTS_DIR/sub01/fmri/bbrumeanSBref_sess1_mp1.nii
> >> volume = 256 256 256
> >> voxelsize = 1.000e+00 1.000e+00
> >> 1.000e+00
> >> xras   = -1.000e+00 0.000e+00
> >> 0.000e+00
> >> yras   = 0.000e+00 0.000e+00
> >> -1.000e+00
> >> zras   = 0.000e+00 1.000e+00
> >> 0.000e+00
> >> cras   = 1.867614746093750e+00 -1.400651550292969e+01
> >> 4.246002197265625e+00
> >> dst volume info
> >> valid = 1  # volume info valid
> >> filename = /SUBJECTS_DIR/sub01/fmri/bbrumeanSBref_sess1_mp1.nii
> >> volume = 256 256 256
> >> voxelsize = 1.000e+00 1.000e+00
> >> 1.000e+00
> >> xras   = -1.000e+00 0.000e+00
> >> 0.000e+00
> >> yras   = 0.000e+00 0.000e+00
> >> -1.000e+00
> >> zras   = 0.000e+00 1.000e+00
> >> 0.000e+00
> >> cras   = 1.867614746093750e+00 -1.400651550292969e+01
> >> 4.246002197265625e+00
> >> subject manat_mp1
> >> fscale 0.15
> >>
> 

Re: [Freesurfer] mask volume calculation

[Douglas N Greve]

The difference is probably due to the partial volume correction, which 
will be different with different segmentations


On 11/06/2017 03:06 PM, Ehsan Tadayon wrote:
> Thanks Bruce
> Thanks Doug
>
> that was a great help. I was able to run it as you mentioned. I also 
> tried to see if I can get the same values as aseg.stats file that you 
> mentioned. I created a binarized mask from aseg.mgz for a structure 
> and ran the same command. However, the values that I get are a little 
> bit different from aseg.stats file. I used mri_segstats as you mentioned.
>
> thanks again for your help.
> best,
> Ehsan.
> ‌
>
> On Sun, Nov 5, 2017 at 1:34 PM, Douglas Greve 
> > wrote:
>
> Look in the recon-all.log file for the command that generates the
> aseg.stats file. Use that command but change aseg.mgz to whatever
> your mask is (and change the output). Don't include the LUT on the
> command line.
>
>
> On 11/1/17 10:24 PM, Ehsan Tadayon wrote:
>> Hello FS experts,
>>
>> I'm trying to get the volume of a binary mask on orig.mgz. I know
>> that FS uses a more sophisitcated approach than simply counting
>> the number of voxels within the mask and I'd like to apply the
>> same approach. Is there any way to get the volume for a defined
>> mask with the same approach that FS computes the volumes for
>> aseg.mgz?
>>
>> thanks.
>> Ehsan
>>
>>
>>
>> ‌
>>
>>
>> ___
>> Freesurfer mailing list
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>> 
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>
>
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> 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.
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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Re: [Freesurfer] surface based fMRI gorup analysis from spm

[Douglas N Greve]

Did you keep the spm output in native functional space?


On 11/07/2017 09:23 AM, Elisa Castaldi wrote:
> Yes,
> this is what I have already done: I moved both the fsaverage and the 
> subjects into SUBJECTS_DIR and the error I get is ERROR: source volume 
> is neither source nor target of the registration.
>
> On 7 November 2017 at 15:11, Douglas Greve  > wrote:
>
> When you look in SUBJECTS_DIR,  you should see fsaverage and all
> the subjects being passed to mris_preproc. If not, you need to
> move them (or sym link them) into that folder.
>
>
> On 11/7/17 6:07 AM, Elisa Castaldi wrote:
>> Thanks for your answer.
>> If I don't specify the directory I get the following error
>> ERROR: cannot find fsaverage in SUBJECTS_DIR
>>
>> and if I move fsaverage to SUBJECTS_DIR it says that it cannot
>> find manat_mp1 which is the name of the folder containing the
>> results of recon all for the subject sub01 (contained in the
>> SUBJECTS_DIR/surfaces folder). If then I move the manat_mp1
>> folder into SUBJECTS_DIR it starts running, but then gives the
>> following error ERROR: source volume is neither source nor target
>> of the registration.
>> Below the entire list of output printed before the error
>>
>> mris_preproc --out lh.con.mgh --target fsaverage --hemi lh \
>> > --iv ${SUBJECTS_DIR}/sub01/stats/con_0001.nii
>> ${SUBJECTS_DIR}/sub01/fmri/mp1reg.lta\
>> nsubjects = 1
>> tmpdir is ./tmp.mris_preproc.30824
>> SUBJECTS_DIR
>> Log file is lh.con.mris_preproc.log
>>
>> setenv SUBJECTS_DIR
>> cd /SUBJECTS_DIR
>> /i2bm/local/freesurfer/bin/mris_preproc --out lh.con.mgh --target
>> fsaverage --hemi lh --iv /SUBJECTS_DIR/sub01/stats/con_0001.nii
>> /SUBJECTS_DIR/sub01/fmri/mp1reg.lta
>>
>> $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $
>> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>> tmpdir is ./tmp.mris_preproc.30824
>> Src lh sphere.reg
>> Trg lh sphere.reg
>>
>> ---
>> #@# 1/1 manat_mp1  --
>> ---
>> mri_vol2surf --src /SUBJECTS_DIR/sub01/stats/con_0001.nii
>> --srcreg /SUBJECTS_DIR/sub01/fmri/mp1reg.lta --hemi lh --out
>> ./tmp.mris_preproc.30824/subjsurfvals.mgh --cortex --noreshape
>> srcvol = SUBJECTS_DIR/sub01/stats/con_0001.nii
>> srcreg = /SUBJECTS_DIR/sub01/fmri/mp1reg.lta
>> srcregold = 0
>> srcwarp unspecified
>> surf = white
>> hemi = lh
>> reshape = 0
>> interp = nearest
>> float2int = round
>> GetProjMax = 0
>> INFO: float2int code = 0
>> Done loading volume
>> Input reg is LTA
>>
>> type  = 0 # LINEAR_VOX_TO_VOX
>> nxforms   = 1
>> mean  = 0. 0. 0.
>> sigma = 1.
>> 1 4 4
>> 9.66621398926e-01 2.551120938733220e-03 5.084594013169408e-04
>> -5.48828125000e-01
>> 4.461563366930932e-04 2.438484877347946e-02
>> -9.997024536132812e-01 2.180384216308594e+02
>> -2.562706125900149e-03 9.996992945671082e-01
>> 2.438353188335896e-02 -5.147048950195312e+00
>> 0.000e+00 0.000e+00 0.000e+00
>> 1.000e+00
>> src volume info
>> valid = 1  # volume info valid
>> filename = /SUBJECTS_DIR/sub01/fmri/bbrumeanSBref_sess1_mp1.nii
>> volume = 256 256 256
>> voxelsize = 1.000e+00 1.000e+00
>> 1.000e+00
>> xras   = -1.000e+00 0.000e+00
>> 0.000e+00
>> yras   = 0.000e+00 0.000e+00
>> -1.000e+00
>> zras   = 0.000e+00 1.000e+00
>> 0.000e+00
>> cras   = 1.867614746093750e+00 -1.400651550292969e+01
>> 4.246002197265625e+00
>> dst volume info
>> valid = 1  # volume info valid
>> filename = /SUBJECTS_DIR/sub01/fmri/bbrumeanSBref_sess1_mp1.nii
>> volume = 256 256 256
>> voxelsize = 1.000e+00 1.000e+00
>> 1.000e+00
>> xras   = -1.000e+00 0.000e+00
>> 0.000e+00
>> yras   = 0.000e+00 0.000e+00
>> -1.000e+00
>> zras   = 0.000e+00 1.000e+00
>> 0.000e+00
>> cras   = 1.867614746093750e+00 -1.400651550292969e+01
>> 4.246002197265625e+00
>> subject manat_mp1
>> fscale 0.15
>>
>> ERROR: source volume is neither source nor target of the registration
>>
>> Any other suggestions?
>> Thanks a lot
>>
>> On 6 November 2017 at 23:42, Douglas N Greve
>> > wrote:
>>
>> Use
>>
>> --target fsaverage
>>
>> instead of giving the full 

Re: [Freesurfer] hemisphere analysis

[Bruce Fischl]

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  
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
  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


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--
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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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
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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.

Re: [Freesurfer] surface based fMRI gorup analysis from spm

[Elisa Castaldi]

Yes,
this is what I have already done: I moved both the fsaverage and the
subjects into SUBJECTS_DIR and the error I get is ERROR: source volume is
neither source nor target of the registration.

On 7 November 2017 at 15:11, Douglas Greve 
wrote:

> When you look in SUBJECTS_DIR,  you should see fsaverage and all the
> subjects being passed to mris_preproc. If not, you need to move them (or
> sym link them) into that folder.
>
> On 11/7/17 6:07 AM, Elisa Castaldi wrote:
>
> Thanks for your answer.
> If I don't specify the directory I get the following error
> ERROR: cannot find fsaverage in SUBJECTS_DIR
>
> and if I move fsaverage to SUBJECTS_DIR it says that it cannot find
> manat_mp1 which is the name of the folder containing the results of recon
> all for the subject sub01 (contained in the SUBJECTS_DIR/surfaces folder).
> If then I move the manat_mp1 folder into SUBJECTS_DIR it starts running,
> but then gives the following error ERROR: source volume is neither source
> nor target of the registration.
> Below the entire list of output printed before the error
>
> mris_preproc --out lh.con.mgh --target fsaverage --hemi lh \
> > --iv ${SUBJECTS_DIR}/sub01/stats/con_0001.nii
> ${SUBJECTS_DIR}/sub01/fmri/mp1reg.lta\
> nsubjects = 1
> tmpdir is ./tmp.mris_preproc.30824
> SUBJECTS_DIR
> Log file is lh.con.mris_preproc.log
>
> setenv SUBJECTS_DIR
> cd /SUBJECTS_DIR
> /i2bm/local/freesurfer/bin/mris_preproc --out lh.con.mgh --target
> fsaverage --hemi lh --iv /SUBJECTS_DIR/sub01/stats/con_0001.nii
> /SUBJECTS_DIR/sub01/fmri/mp1reg.lta
>
> $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> tmpdir is ./tmp.mris_preproc.30824
> Src lh sphere.reg
> Trg lh sphere.reg
>
> ---
> #@# 1/1 manat_mp1  --
> ---
> mri_vol2surf --src /SUBJECTS_DIR/sub01/stats/con_0001.nii --srcreg
> /SUBJECTS_DIR/sub01/fmri/mp1reg.lta --hemi lh --out
> ./tmp.mris_preproc.30824/subjsurfvals.mgh --cortex --noreshape
> srcvol = SUBJECTS_DIR/sub01/stats/con_0001.nii
> srcreg = /SUBJECTS_DIR/sub01/fmri/mp1reg.lta
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = lh
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> Done loading volume
> Input reg is LTA
>
> type  = 0 # LINEAR_VOX_TO_VOX
> nxforms   = 1
> mean  = 0. 0. 0.
> sigma = 1.
> 1 4 4
> 9.66621398926e-01 2.551120938733220e-03 5.084594013169408e-04
> -5.48828125000e-01
> 4.461563366930932e-04 2.438484877347946e-02 -9.997024536132812e-01
> 2.180384216308594e+02
> -2.562706125900149e-03 9.996992945671082e-01 2.438353188335896e-02
> -5.147048950195312e+00
> 0.000e+00 0.000e+00 0.000e+00
> 1.000e+00
> src volume info
> valid = 1  # volume info valid
> filename = /SUBJECTS_DIR/sub01/fmri/bbrumeanSBref_sess1_mp1.nii
> volume = 256 256 256
> voxelsize = 1.000e+00 1.000e+00
> 1.000e+00
> xras   = -1.000e+00 0.000e+00 0.000e+00
> yras   = 0.000e+00 0.000e+00 -1.000e+00
> zras   = 0.000e+00 1.000e+00 0.000e+00
> cras   = 1.867614746093750e+00 -1.400651550292969e+01 4.246002197265625e+00
> dst volume info
> valid = 1  # volume info valid
> filename = /SUBJECTS_DIR/sub01/fmri/bbrumeanSBref_sess1_mp1.nii
> volume = 256 256 256
> voxelsize = 1.000e+00 1.000e+00
> 1.000e+00
> xras   = -1.000e+00 0.000e+00 0.000e+00
> yras   = 0.000e+00 0.000e+00 -1.000e+00
> zras   = 0.000e+00 1.000e+00 0.000e+00
> cras   = 1.867614746093750e+00 -1.400651550292969e+01 4.246002197265625e+00
> subject manat_mp1
> fscale 0.15
>
> ERROR: source volume is neither source nor target of the registration
>
> Any other suggestions?
> Thanks a lot
>
> On 6 November 2017 at 23:42, Douglas N Greve 
> wrote:
>
>> Use
>>
>> --target fsaverage
>>
>> instead of giving the full path
>>
>>
>> On 11/06/2017 01:27 PM, Elisa Castaldi wrote:
>> > Dear Freesurfer users,
>> >
>> > I would like to perform surface based fMRI gorup analysis in
>> > Freesurfer starting from SPM first level output files, but I am not
>> > succeding.
>> > I have already preprocessed the data in spm and used Freesurfer for
>> > boundary based registration, I have succesfully ran the recon -all
>> > comand and ovelayed the first level analysis output file (created with
>> > spm).
>> >
>> > Now I would like to perform surface based fMRI group analysis with
>> > Freesurfer, but I am worried it is crashing either because the folders
>> > are not organized the way they should or because I am missing some
>> files.
>> >
>> > first I have 

Re: [Freesurfer] surface based fMRI gorup analysis from spm

[Douglas Greve]

When you look in SUBJECTS_DIR,  you should see fsaverage and all the 
subjects being passed to mris_preproc. If not, you need to move them (or 
sym link them) into that folder.



On 11/7/17 6:07 AM, Elisa Castaldi wrote:

Thanks for your answer.
If I don't specify the directory I get the following error
ERROR: cannot find fsaverage in SUBJECTS_DIR

and if I move fsaverage to SUBJECTS_DIR it says that it cannot find 
manat_mp1 which is the name of the folder containing the results of 
recon all for the subject sub01 (contained in the 
SUBJECTS_DIR/surfaces folder). If then I move the manat_mp1 folder 
into SUBJECTS_DIR it starts running, but then gives the following 
error ERROR: source volume is neither source nor target of the 
registration.

Below the entire list of output printed before the error

mris_preproc --out lh.con.mgh --target fsaverage --hemi lh \
> --iv ${SUBJECTS_DIR}/sub01/stats/con_0001.nii 
${SUBJECTS_DIR}/sub01/fmri/mp1reg.lta\

nsubjects = 1
tmpdir is ./tmp.mris_preproc.30824
SUBJECTS_DIR
Log file is lh.con.mris_preproc.log

setenv SUBJECTS_DIR
cd /SUBJECTS_DIR
/i2bm/local/freesurfer/bin/mris_preproc --out lh.con.mgh --target 
fsaverage --hemi lh --iv /SUBJECTS_DIR/sub01/stats/con_0001.nii 
/SUBJECTS_DIR/sub01/fmri/mp1reg.lta


$Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
tmpdir is ./tmp.mris_preproc.30824
Src lh sphere.reg
Trg lh sphere.reg

---
#@# 1/1 manat_mp1  --
---
mri_vol2surf --src /SUBJECTS_DIR/sub01/stats/con_0001.nii --srcreg 
/SUBJECTS_DIR/sub01/fmri/mp1reg.lta --hemi lh --out 
./tmp.mris_preproc.30824/subjsurfvals.mgh --cortex --noreshape

srcvol = SUBJECTS_DIR/sub01/stats/con_0001.nii
srcreg = /SUBJECTS_DIR/sub01/fmri/mp1reg.lta
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Input reg is LTA

type  = 0 # LINEAR_VOX_TO_VOX
nxforms   = 1
mean  = 0. 0. 0.
sigma = 1.
1 4 4
9.66621398926e-01 2.551120938733220e-03 5.084594013169408e-04 
-5.48828125000e-01
4.461563366930932e-04 2.438484877347946e-02 -9.997024536132812e-01 
2.180384216308594e+02
-2.562706125900149e-03 9.996992945671082e-01 2.438353188335896e-02 
-5.147048950195312e+00
0.000e+00 0.000e+00 0.000e+00 
1.000e+00

src volume info
valid = 1  # volume info valid
filename = /SUBJECTS_DIR/sub01/fmri/bbrumeanSBref_sess1_mp1.nii
volume = 256 256 256
voxelsize = 1.000e+00 1.000e+00 
1.000e+00
xras   = -1.000e+00 0.000e+00 
0.000e+00
yras   = 0.000e+00 0.000e+00 
-1.000e+00

zras   = 0.000e+00 1.000e+00 0.000e+00
cras   = 1.867614746093750e+00 -1.400651550292969e+01 
4.246002197265625e+00

dst volume info
valid = 1  # volume info valid
filename = /SUBJECTS_DIR/sub01/fmri/bbrumeanSBref_sess1_mp1.nii
volume = 256 256 256
voxelsize = 1.000e+00 1.000e+00 
1.000e+00
xras   = -1.000e+00 0.000e+00 
0.000e+00
yras   = 0.000e+00 0.000e+00 
-1.000e+00

zras   = 0.000e+00 1.000e+00 0.000e+00
cras   = 1.867614746093750e+00 -1.400651550292969e+01 
4.246002197265625e+00

subject manat_mp1
fscale 0.15

ERROR: source volume is neither source nor target of the registration

Any other suggestions?
Thanks a lot

On 6 November 2017 at 23:42, Douglas N Greve 
> wrote:


Use

--target fsaverage

instead of giving the full path


On 11/06/2017 01:27 PM, Elisa Castaldi wrote:
> Dear Freesurfer users,
>
> I would like to perform surface based fMRI gorup analysis in
> Freesurfer starting from SPM first level output files, but I am not
> succeding.
> I have already preprocessed the data in spm and used Freesurfer for
> boundary based registration, I have succesfully ran the recon -all
> comand and ovelayed the first level analysis output file
(created with
> spm).
>
> Now I would like to perform surface based fMRI group analysis with
> Freesurfer, but I am worried it is crashing either because the
folders
> are not organized the way they should or because I am missing
some files.
>
> first I have converted .dat into .lta file
> tkregister --mov bbrumeanSBref_sess1_mp1.nii --targ
> bbrumeanSBref_sess1_mp1.nii --reg bbrumeanSBref_sess1_mp1.dat
--ltaout
> mp1reg.lta --noedi
>
> then
> mris_preproc --out lh.con.mgh --target
> ${SUBJECTS_DIR}/surfaces/fsaverage --hemi lh \
>     --iv ${SUBJECTS_DIR}/sub01/stats/con_0001.nii
> 

Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

[Douglas Greve]

The way that mris_preproc used to work was confusing. It made it look 
like you were actually sampling to my_subject_average. In reality, it 
was only using my_subject_average to perform smoothing -- the entire 
analysis was done in fsaverage space. To clarify this, I required that 
there by a new surface registration file when something other than 
fsaverage is specified as the target. If you want to perform the 
analysis in my_subject_average, then run the surfreg script for each 
subject targeting my_subject_average. If you want to do it as before, 
then use fsaverage. You can visualize the results on my_subject_average.




On 11/7/17 8:02 AM, M del Mar Velasco wrote:


Dear FreeSurfer experts,


I am using /mris_preproc/ command with following options:


/mris_preproc --s s_001 --s s_002 --s s_003 --target 
my_subject_average --hemi lh --meas my_input_surf.mgh --out 
/my_output_path/output_file/



I observe/mris_preproc/ uses /mri_surf2surf/. My question is related 
to Freesurfer version. Using FreeSurfer 5.3, /mri_surf2surf/ takes 
/sphere.reg/ as /srcsurfreg/, while with Freesurfer 6 script 
/mri_surf2surf/ has changed. It takes /my_subject_average.sphere.reg 
/(target of /mris_preproc/) as /s//rcsurfreg/. I get an error because 
/my_subject_average.sphere.reg/ file doesn't exist inside s_001 folder.



Why Freesurfer 6 changes /srcsurfreg/ to /$target.sphere.reg/? What 
can I do in order to be coherent with my script which was designed 
using Freesurfer 5.3?



Thanks in advance,


M del Mar




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Re: [Freesurfer] hemisphere analysis

[Douglas Greve]

I have no idea what that means. can you explain?


On 11/7/17 12:02 AM, 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 
> 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

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


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--
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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the e-mail
contains patient information, please contact the Partners Compliance 
HelpLine at
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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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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

[M del Mar Velasco]

Dear FreeSurfer experts,


I am using mris_preproc command with following options:


 mris_preproc --s s_001 --s s_002 --s s_003 --target my_subject_average 
--hemi lh --meas my_input_surf.mgh --out /my_output_path/output_file


I observe mris_preproc uses mri_surf2surf. My question is related to Freesurfer 
version. Using FreeSurfer 5.3, mri_surf2surf takes sphere.reg as srcsurfreg, 
while with Freesurfer 6 script mri_surf2surf has changed. It takes 
my_subject_average.sphere.reg (target of mris_preproc) as srcsurfreg. I get an 
error because my_subject_average.sphere.reg file doesn't exist inside s_001 
folder.


Why Freesurfer 6 changes srcsurfreg to $target.sphere.reg? What can I do in 
order to be coherent with my script which was designed using Freesurfer 5.3?


Thanks in advance,


M del Mar



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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] surface based fMRI gorup analysis from spm

[Elisa Castaldi]

Thanks for your answer.
If I don't specify the directory I get the following error
ERROR: cannot find fsaverage in SUBJECTS_DIR

and if I move fsaverage to SUBJECTS_DIR it says that it cannot find
manat_mp1 which is the name of the folder containing the results of recon
all for the subject sub01 (contained in the SUBJECTS_DIR/surfaces folder).
If then I move the manat_mp1 folder into SUBJECTS_DIR it starts running,
but then gives the following error ERROR: source volume is neither source
nor target of the registration.
Below the entire list of output printed before the error

mris_preproc --out lh.con.mgh --target fsaverage --hemi lh \
> --iv ${SUBJECTS_DIR}/sub01/stats/con_0001.nii
${SUBJECTS_DIR}/sub01/fmri/mp1reg.lta\
nsubjects = 1
tmpdir is ./tmp.mris_preproc.30824
SUBJECTS_DIR
Log file is lh.con.mris_preproc.log

setenv SUBJECTS_DIR
cd /SUBJECTS_DIR
/i2bm/local/freesurfer/bin/mris_preproc --out lh.con.mgh --target fsaverage
--hemi lh --iv /SUBJECTS_DIR/sub01/stats/con_0001.nii
/SUBJECTS_DIR/sub01/fmri/mp1reg.lta

$Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
tmpdir is ./tmp.mris_preproc.30824
Src lh sphere.reg
Trg lh sphere.reg

---
#@# 1/1 manat_mp1  --
---
mri_vol2surf --src /SUBJECTS_DIR/sub01/stats/con_0001.nii --srcreg
/SUBJECTS_DIR/sub01/fmri/mp1reg.lta --hemi lh --out
./tmp.mris_preproc.30824/subjsurfvals.mgh --cortex --noreshape
srcvol = SUBJECTS_DIR/sub01/stats/con_0001.nii
srcreg = /SUBJECTS_DIR/sub01/fmri/mp1reg.lta
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Input reg is LTA

type  = 0 # LINEAR_VOX_TO_VOX
nxforms   = 1
mean  = 0. 0. 0.
sigma = 1.
1 4 4
9.66621398926e-01 2.551120938733220e-03 5.084594013169408e-04
-5.48828125000e-01
4.461563366930932e-04 2.438484877347946e-02 -9.997024536132812e-01
2.180384216308594e+02
-2.562706125900149e-03 9.996992945671082e-01 2.438353188335896e-02
-5.147048950195312e+00
0.000e+00 0.000e+00 0.000e+00
1.000e+00
src volume info
valid = 1  # volume info valid
filename = /SUBJECTS_DIR/sub01/fmri/bbrumeanSBref_sess1_mp1.nii
volume = 256 256 256
voxelsize = 1.000e+00 1.000e+00
1.000e+00
xras   = -1.000e+00 0.000e+00 0.000e+00
yras   = 0.000e+00 0.000e+00 -1.000e+00
zras   = 0.000e+00 1.000e+00 0.000e+00
cras   = 1.867614746093750e+00 -1.400651550292969e+01 4.246002197265625e+00
dst volume info
valid = 1  # volume info valid
filename = /SUBJECTS_DIR/sub01/fmri/bbrumeanSBref_sess1_mp1.nii
volume = 256 256 256
voxelsize = 1.000e+00 1.000e+00
1.000e+00
xras   = -1.000e+00 0.000e+00 0.000e+00
yras   = 0.000e+00 0.000e+00 -1.000e+00
zras   = 0.000e+00 1.000e+00 0.000e+00
cras   = 1.867614746093750e+00 -1.400651550292969e+01 4.246002197265625e+00
subject manat_mp1
fscale 0.15

ERROR: source volume is neither source nor target of the registration

Any other suggestions?
Thanks a lot

On 6 November 2017 at 23:42, Douglas N Greve 
wrote:

> Use
>
> --target fsaverage
>
> instead of giving the full path
>
>
> On 11/06/2017 01:27 PM, Elisa Castaldi wrote:
> > Dear Freesurfer users,
> >
> > I would like to perform surface based fMRI gorup analysis in
> > Freesurfer starting from SPM first level output files, but I am not
> > succeding.
> > I have already preprocessed the data in spm and used Freesurfer for
> > boundary based registration, I have succesfully ran the recon -all
> > comand and ovelayed the first level analysis output file (created with
> > spm).
> >
> > Now I would like to perform surface based fMRI group analysis with
> > Freesurfer, but I am worried it is crashing either because the folders
> > are not organized the way they should or because I am missing some files.
> >
> > first I have converted .dat into .lta file
> > tkregister --mov bbrumeanSBref_sess1_mp1.nii --targ
> > bbrumeanSBref_sess1_mp1.nii --reg bbrumeanSBref_sess1_mp1.dat --ltaout
> > mp1reg.lta --noedi
> >
> > then
> > mris_preproc --out lh.con.mgh --target
> > ${SUBJECTS_DIR}/surfaces/fsaverage --hemi lh \
> > --iv ${SUBJECTS_DIR}/sub01/stats/con_0001.nii
> > ${SUBJECTS_DIR}/sub01/fmri/mp1reg.lta\
> > --iv ${SUBJECTS_DIR}/sub02/stats/con_0001.nii
> > ${SUBJECTS_DIR}/sub02/fmri/ab1reg.lta\
> > --projfrac 0.5 \
> >
> > ERROR: cannot find SUBJECTS_DIR/surfaces/fsaverage in SUBJECTS_DIR
> >
> > Trying to move files in the requested directory caused other errors,
> > everytime not finding what it needs.
> >
> >