Re: [Freesurfer] Myelinated cortical thickness ratio map

[Greve, Douglas N.,Ph.D.]

You can use the per-voxel regressor (--pvr) option to mri_glmfit. Search 
through the mail archives for how to use it

On 10/23/2018 06:34 AM, Damien MARIE wrote:
>
> External Email - Use Caution
>
> Hi Matt,
>
> Many thanks for your prompt reply, you are right.
>
> Any tips on how I could do that?
>
> Should I regress out cortical thickness from my myelin maps at the 
> individual level, save the individual output myelin maps and run 
> analyses on the latter? If yes how?
>
> That’s really important to me otherwise a reviewer could claim the 
> myelin differences we detect might be supported by cortical thickness 
> variations and not myelin…
>
> Thank you and best,
>
> Damien
>
>
>
>> Glasser, Matthew 
>> Mon,
>>  
>> 22 Oct 2018 12:57:43 -0700 
>> 
>>
>> Regression would be better than division.
>> Matt.
>>
>> From:
>> > >
>>   on behalf of Damien MARIE http://damien.ma/>...@unige.ch 
>> >
>> Reply-To: Freesurfer support list
>> > >
>> Date: Monday, October 22, 2018 at 8:54 AM
>> To: "freesurfer@nmr.mgh.harvard.edu 
>> "
>>  
>> > >
>> Subject: [Freesurfer] Myelinated cortical thickness ratio map
>>
>>
>>  External Email - Use Caution
>>
>> Dear experts,
>>
>> I am working with R1 maps that I project on the surface. The goal is to look 
>> at
>> intra-cortical myelin.
>>
>> I detect interesting effects between two groups. Now I would like to compute
>> myelinated cortical thickness ratio maps, in order to control for the effect 
>> of
>> cortical thickness variations occurring with gyrification.
>>
>> Here is a paper where they describe a way to compute those myelinated 
>> cortical
>> thickness ratio map with MIPAV and the MPI-CBS toolbox :
>> https://www.ncbi.nlm.nih.gov/pubmed/29321232
>> «  The proportional thickness of the myelinated part of the cortex in 
>> relation
>> to its overall thickness (myelinated cortical thickness) was computed with a
>> fuzzy classification technique combining information about radial and
>> tangential fibers.  «
>>
>> 1- Is it possible to do the same in FreeSurfer?
>>
>> 2- What about dividing my individual myelin maps by the individual cortical
>> thickness maps? Is it possible to do that in FreeSurfer? SPM ImCalc would do
>> the job in the volume but I don’t know how I could do that in FreeSurfer.
>>
>> Any comments / other suggestions are welcome.
>>
>> Thank you and best,
>>
>> Damien
>>
>
>
>
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Re: [Freesurfer] Paired Analysis Contrasts

[Greve, Douglas N.,Ph.D.]

On 10/24/2018 09:45 PM, srishti goel wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I am trying to perform a paired analysis for a data set that has 
> subjects' who belong to either group1 or group2 and have data at time 
> point1 (tp1) and time point2 (tp2). I am following all the steps on 
> the wiki but I want to clarify if the contrasts I plan to use for my 
> analyses are appropriate.
>
> For my analyses, I only have two groups and no covariates. I am 
> interested to know if the decrease in cortical thickness of subjects 
> in group 1 across tp1 and tp2 is more than the decrease in cortical 
> thickness of subjects in group 2 across tp1 and tp2. The contrast I 
> think should be used for this is: 1 -1. Is that correct?
Yes, if you first take the difference between tp1 and tp2.
>
> I am also interested to know if the cortical thickness decreased for 
> subjects regardless of the groups so should I use the contrast: 1 for 
> that?
Assuming you are keeping 2 groups, then use
  0.5 0.5
>
> Best,
> Srishti
> Social/Clinical Research Specialist
> Child Imaging Research and Life Experiences Lab
> University of North Carolina at Chapel Hill
> email (W): srish...@email.unc.edu 
> skype: srishti.goel12
>
>
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Re: [Freesurfer] Mapping a custom measure to the pial surface of fsaverage

[Greve, Douglas N.,Ph.D.]

On 10/25/2018 11:31 AM, ts...@rcmd.org wrote:
>  External Email - Use Caution
>
> Dear Douglas,
>
> thanks for your answer.
>
> Did you by any chance mean mris_preproc instead of preproc-sess? The latter 
> seems to have no --meas flag according to the help (and a quick grep through 
> the script file).
Yes, sorry.
>
> I ended up placing the curv files in /surf/?h..pial and the running:
> recon-all -s $SUBJECT -qcache -no-isrunning -measure ${MEASURE}.pial
>
> This seems to also have done the trick, and it seems to be the way it is done 
> by recon-all for the area.
That should work, but you should have been able to use mris_preproc 
directly (recon-all just calls mris_preproc).
>
> I only expected that you have to explicitly define that the values should be 
> mapped to the pial surface of the fsaverage subject. But if vertex #n in the 
> pial is the closest vertex to vertex #n in the white, maybe no special 
> handling is needed?
Right, the white and the pail use the same registratin
>
> Tim
>
>> On October 23, 2018 at 6:08 PM "Greve, Douglas N.,Ph.D." 
>>  wrote:
>>
>>
>> You can use preproc-sess and specify the --meas flag. Run with --help
>> for more info.
>>
>> On 10/18/18 2:08 PM, ts...@rcmd.org wrote:
>>>   External Email - Use Caution
>>>
>>> Dear FreeSurfer experts,
>>>
>>> I have created a custom measure on the pial surface of a number of 
>>> subjects, and I would like to map the data to the fsaverage subject. (By 
>>> custom measure I mean something like 'area' or 'curv', i.e., one scalar 
>>> value per surface vertex.)
>>>
>>> I have already done the same for the white surfaces, and it was pretty 
>>> straight-forward:
>>> 1) Save the per-vertex data in a curv-format file in 
>>> SUBJECTS_DIR//surf/?h.
>>> 2) Run 'recon-all -s  -qcache -measure '
>>>
>>> This will map the data to fsaverage and create files named 
>>> ?h..fwhm.fsaverage.mgh in the surf/ directories as expected 
>>> (where  is 0, 5, .., 25).
>>>
>>> My question is: how can I do the same for my data from the pial surface? 
>>> Are there any command line options for 'recon-all' (or maybe for 
>>> mris_preproc) that can do this?
>>>
>>> I already tried to put the pial per-vertex data into files named 
>>> SUBJECTS_DIR//surf/?h.pial., but they are not handled by 
>>> the recon-all command listed above: no fsaverage files show up for them.
>>>
>>> Thanks in advance,
>>>
>>> Tim
>>>
>>> --
>>> Dr. Tim Schäfer
>>> Postdoc Computational Neuroimaging
>>> Department of Child and Adolescent Psychiatry, Psychosomatics and 
>>> Psychotherapy
>>> University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
>>>
>>> ___
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>>
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Dr. Tim Schäfer
> Postdoc Computational Neuroimaging
> Department of Child and Adolescent Psychiatry, Psychosomatics and 
> Psychotherapy
> University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
>
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Re: [Freesurfer] First level modelling in task-based fMRI data

[Greve, Douglas N.,Ph.D.]

On 10/26/2018 10:53 AM, Zhi Li wrote:
>
> External Email - Use Caution
>
> Hi FreeSurfer Experts,
>
> Now I am trying FS-FAST in analyzing task-based fMRI data. We have two 
> runs for each participant. However, there were not enough events in 
> some runs of some participants. Hence we'd like to concatenate the 
> preprocessed images of two runs into one rather than model them 
> separately. How can we combine the preprocessed surface and 
> sub-cortical data of each run into one?
This happens automatically. Just make sure the paradigm files are correct.
>
> In addition. can we use FreeSurfer or FS-FAST to analyse task-based 
> functional connections, such as psychophysiological interactions 
> analysis and dynamic causal modelling? Do you have any suggestions?
Sorry, this is not offered in FSFAST. You can try this toolbox 
https://www.nitrc.org/projects/gppi (I have not used it before, so I 
can't say how well it works).
>
> Thank you and best wishes,
>
> Zhi
>
>
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Re: [Freesurfer] freesurfer selxavg3-sess error

[Greve, Douglas N.,Ph.D.]

When you ran mkanalysis-sess, did you specify two event types? You only 
have one non-null event in your paradigm file.

On 10/28/2018 08:57 AM, Francesca Strappini wrote:
>
> External Email - Use Caution
>
> Thanks! Now it's loading correctly my event file.
> However, when I run selxavg3-sess I get this error message:
>
> selxavg3-sess -a FF-MonkeyCassis.sm03.lh -s MonkeyCassis-FF -no-con-ok
>
> outanadir = 
> /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF/bold/FF-MonkeyCassis.sm03.lh
> Excluding 2 points
> Excluding 2 points
> Excluding 2 points
> Excluding 2 points
> Excluding 2 points
> Excluding 2 points
> Excluding 2 points
> Excluding 2 points
> Excluding 2 points
> Excluding 2 points
> parfiles condition id list:  1
> ERROR: found 1 non-null conditions, expected 2
> --
> ERROR: fast_selxavg3() failed\n
>
> This is my even file:
>
> 0    1    32    1    ON
> 32    0    32    1    OFF
> 64    1    32    1    ON
> 96    0    32    1    OFF
> 128    1    32    1    ON
> 160    0    32    1    OFF
> 192    1    32    1    ON
> 224    0    32    1    OFF
>
> Thanks for the help!
> Best
> Francesca
>
> Il giorno gio 3 mag 2018 alle ore 00:49 Douglas N. Greve 
> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>
> oops, sorry. Looks like it is having a problem loading your paradigm
> file. Check that. If the error does not pop out to you then send
> it to me.
>
>
> On 05/02/2018 10:06 AM, Francesca Strappini wrote:
> > Hi, sorry, maybe my last email got lost. Is there anything I can
> try
> > to fix this problem with selxavg3-sess?
> >
> > Thanks!
> > Best
> > Francesca
> >
> > 2018-04-24 20:35 GMT+03:00 Francesca Strappini
> >  
>  >>:
> >
> >     Thank you for the reply!
> >     I deleted the contrasts and run this command line:
> >
> >     selxavg3-sess -a FF-MonkeyCassis.sm03.rh -s MonkeyCassis-FF
> -no-con-ok
> >
> >
> >     --- matlab output 
> >     MATLAB is selecting SOFTWARE OPENGL rendering.
> >
> >     < M A T L A B (R) >
> >       Copyright 1984-2016 The MathWorks, Inc.
> >        R2016b (9.1.0.441655) 64-bit (glnxa64)
> >      September 7, 2016
> >
> >
> >     To get started, type one of these: helpwin, helpdesk, or demo.
> >     For product information, visit www.mathworks.com
> 
> >     .
> >
> >     >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
> >     >> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
> >     >> /usr/local/freesurfer/matlab/MRIread.m
> >     >> >> >> starting fast_selxavg3b
> >
> >
> >     #@# MonkeyCassis-FF ###
> >     /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF
> >     -
> >     $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
> >     -
> >     outtop = /usr/local/freesurfer/fsfast/Monkeys
> >     Extension format = nii.gz
> >     INFO: key nSliceGroups unrecognized, line 11, skipping
> >     Subscripted assignment dimension mismatch.
> >
> >     Error in fast_ldpar4 (line 97)
> >       par4(nthrow,1) = tonset;
> >
> >     Error in flac_customize (line 121)
> >     [par partype] = fast_ldpar4(parpath);
> >
> >     Error in fast_selxavg3b (line 129)
> >     flac0 = flac_customize(flac0);
> >
> >     >> --
> >     ERROR: fast_selxavg3() failed\n
> >
> >
> >     2018-04-24 20:27 GMT+03:00 Douglas Greve
> mailto:dgr...@mgh.harvard.edu>
> >      >>:
> >
> >         Try deleting the contrasts (.mat files) and rerunning
> >
> >
> >         On 4/24/18 5:48 AM, Francesca Strappini wrote:
> >>
> >>
> >>         Dear FreeSurfer experts,
> >>
> >>         I'm trying to analyze some monkey functional data. I
> got this
> >>         error message with selxavg3-sess.
> >>
> >>         I run the following commands:
> >>
> >>         mkcontrast-sess -analysis FF-MonkeyCassis.sm03.lh -contrast
> >>         ON-vs-OFF -a 1 -c 0
> >>         mkcontrast-sess -analysis FF-MonkeyCassis.sm03.rh -contrast
> >>         ON-vs-OFF -a 1 -c 0
> >>         preproc-sess -surface MonkeyCassis lhrh -fwhm 3 -s
> >>         MonkeyCassis-FF -fsd bold -per-session
> >>         selxavg3-sess -a FF-MonkeyCassis.sm03.lh -s MonkeyCassis-FF
> >>
> >>
> >>         --- matlab output 

Re: [Freesurfer] aparcstats2table --parcs-from-file trouble

[Greve, Douglas N.,Ph.D.]

If you are using output froom mri_segstats, then you need to use 
asegstats2table, not aparcstats2table. It can be confusing ...

On 11/01/2018 05:06 PM, Figueiro Longo, Maria Gabriela wrote:
>
> Hi,
>
>
> I extracted some volumes using mri_annotation2lable --> mri_aparc2aseg 
> --> mri_segstats .
>
> Now I am trying to extract the summary table using aparcstats2table 
> --parcs-from-file , but every time an error message pops up:
>
>
> ERROR: cannot read 
>
>
> The stats files generated by the mri_segstats look correct (similar 
> with the other files in the directory) and I can read the volumes of 
> each individual.
>
>
> The last command that has an error is:
>
>
> aparcstats2table --qdec-long qdec.txt --hemi lh --meas volume 
> --parcs-from-file  --tablefile volumes.txt
>
>
> I really appreciate any help!
>
> Thanks!
>
> Gabriela
>
>
>
>
>
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Re: [Freesurfer] GLM

[Greve, Douglas N.,Ph.D.]

Use the first one. Not sure what you mean by your multiple comparisons 
question

On 11/01/2018 11:20 PM, 郑凤莲 wrote:
>
> External Email - Use Caution
>
> Hi experts,
>
> I am using FS 6.0 for analyzing the cortical thickness difference 
> between 3 groups: patient1, patient2 and control. In DODS model, I 
> need to creat 2 files, FSDG and mtx file. And we have 3 variables: 
> age, gender and cortical thickness.
> 1. The FSDG file is:
> GroupDescriptorFile 1
> Title Tutorial
> Class patient1-male
> Class patient1-female
> Class patient2-male
> Class patient2-female
> Class control-male
> Class control-female
> Variables                                 age
> Input subject1 patient1-female 20
> Input subject2 patient1-male    33
> Input subject3 patient2-female 40
> Input subject4 patient2-male    50
> Input subject5 control-male    30
> Input subject6 control-female 35
> And there is another way:
> GroupDescriptorFile 1
> Title Tutorial
> Class patient1
> Class patient2
> Class control
> Variables                     sex age
> Input subject1 patient1 1   20
> Input subject2 patient1 2   33
> Input subject3 patient2 1   40
> Input subject4 patient2 2   50
> Input subject5 control   2   30
> Input subject6 control   1   35
> What I want to confirm is that if I want to adjust for sex and age, 
> which one is right?
> Another question is that is there any way to get the multiple 
> comparisons between groups simultaneously?
> I am looking forward to your reply. Thanks very much.
>
> Sincerely,
> Zheng
>
>
>
>
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[Freesurfer] applying the same edits to multiple scans

[Hanford, Lindsay C]

Hello Freesurfer Experts,


I am wondering whether it is possible to apply the same manual edits (removing 
GM/WM or adding CPs) to multiple scans. I have a dataset with ~100 scans per 
subject acquired in quick succession and, interestingly, Freesurfer appears to 
have the same issue in almost all of the scans (I guess that speaks to the 
reliability!). In this case, a small region of the optic nerve is being 
included as GM (and occasionally WM) so I am wondering whether I can reduce my 
time with manual edits by either (1) applying the same edits to multiple 
images, or (2) in this case, applying a more constrained mask to remove the 
possibility of including optic nerve within the brainmask.


Thank you in advance,

Lindsay


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Re: [Freesurfer] Extracting values from a single vertex

[Bruce Fischl]

Hi Ryan

it would be pretty trivial to do in matlab, so probably that is best, 
although I don't understand what multi-frame volume you are using


cheers
Bruce
On Wed, 
7 Nov 2018, Nillo, Ryan Michael R wrote:




External Email - Use Caution

Hi FreeSurfer users,


I want to extract thickness values at a single vertex. I searched on the 
support list and found an
mris_convert command to use. However, the file I want to extract values from is 
a volume with
multiple frames. When I try to use mris_convert on it, I only got the value at 
a vertex on the first
frame. The goal is to set that vertex as a seed point and use the values as a 
regressor for glm. Is
there a way to do this with FreeSurfer's commandline tools, or should I do this 
in Matlab? 


Mahalo,


Ryan M Nillo

Staff Research Associate I

UCSF Department of Radiology and Biomedical Imaging


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Re: [Freesurfer] Mapping a custom measure to the pial surface of fsaverage

[ts+ml]

External Email - Use Caution

Thanks for your time and the clarification.

Tim

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany


> On November 7, 2018 at 3:28 PM "Greve, Douglas N.,Ph.D." 
>  wrote:
> 
> 
> 
> 
> On 10/25/2018 11:31 AM, ts...@rcmd.org wrote:
> >  External Email - Use Caution
> >
> > Dear Douglas,
> >
> > thanks for your answer.
> >
> > Did you by any chance mean mris_preproc instead of preproc-sess? The latter 
> > seems to have no --meas flag according to the help (and a quick grep 
> > through the script file).
> Yes, sorry.
> >
> > I ended up placing the curv files in /surf/?h..pial and the 
> > running:
> > recon-all -s $SUBJECT -qcache -no-isrunning -measure ${MEASURE}.pial
> >
> > This seems to also have done the trick, and it seems to be the way it is 
> > done by recon-all for the area.
> That should work, but you should have been able to use mris_preproc 
> directly (recon-all just calls mris_preproc).
> >
> > I only expected that you have to explicitly define that the values should 
> > be mapped to the pial surface of the fsaverage subject. But if vertex #n in 
> > the pial is the closest vertex to vertex #n in the white, maybe no special 
> > handling is needed?
> Right, the white and the pail use the same registratin
> >
> > Tim
> >
> >> On October 23, 2018 at 6:08 PM "Greve, Douglas N.,Ph.D." 
> >>  wrote:
> >>
> >>
> >> You can use preproc-sess and specify the --meas flag. Run with --help
> >> for more info.
> >>
> >> On 10/18/18 2:08 PM, ts...@rcmd.org wrote:
> >>>   External Email - Use Caution
> >>>
> >>> Dear FreeSurfer experts,
> >>>
> >>> I have created a custom measure on the pial surface of a number of 
> >>> subjects, and I would like to map the data to the fsaverage subject. (By 
> >>> custom measure I mean something like 'area' or 'curv', i.e., one scalar 
> >>> value per surface vertex.)
> >>>
> >>> I have already done the same for the white surfaces, and it was pretty 
> >>> straight-forward:
> >>> 1) Save the per-vertex data in a curv-format file in 
> >>> SUBJECTS_DIR//surf/?h.
> >>> 2) Run 'recon-all -s  -qcache -measure '
> >>>
> >>> This will map the data to fsaverage and create files named 
> >>> ?h..fwhm.fsaverage.mgh in the surf/ directories as expected 
> >>> (where  is 0, 5, .., 25).
> >>>
> >>> My question is: how can I do the same for my data from the pial surface? 
> >>> Are there any command line options for 'recon-all' (or maybe for 
> >>> mris_preproc) that can do this?
> >>>
> >>> I already tried to put the pial per-vertex data into files named 
> >>> SUBJECTS_DIR//surf/?h.pial., but they are not handled 
> >>> by the recon-all command listed above: no fsaverage files show up for 
> >>> them.
> >>>
> >>> Thanks in advance,
> >>>
> >>> Tim
> >>>
> >>> --
> >>> Dr. Tim Schäfer
> >>> Postdoc Computational Neuroimaging
> >>> Department of Child and Adolescent Psychiatry, Psychosomatics and 
> >>> Psychotherapy
> >>> University Hospital Frankfurt, Goethe University Frankfurt am Main, 
> >>> Germany
> >>>
> >>> ___
> >>> Freesurfer mailing list
> >>> Freesurfer@nmr.mgh.harvard.edu
> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > --
> > Dr. Tim Schäfer
> > Postdoc Computational Neuroimaging
> > Department of Child and Adolescent Psychiatry, Psychosomatics and 
> > Psychotherapy
> > University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
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Re: [Freesurfer] How to combine and divide surface-based fMRI data?

[Greve, Douglas N.,Ph.D.]

Are you using FSFAST? If you run the  preprocessing (preproc-sess), then 
it will get you most of the way there.

On 11/05/2018 10:16 AM, Zhi Li wrote:
>
> External Email - Use Caution
>
> Hello FreeSurfer experts,
>
> May I ask how can I modify the surface-based fMRI data, such as 
> combing two independent sessions into one or dividing one 4D into a 
> series of 3D surface-based fMRI files in which each one denotes a 
> single volume/TR? Thank you very much.
>
> Best wishes,
>
> Zhi
>
>
> ___
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[Freesurfer] MatrixReadTxT: could not scan value [1][1]

[Anwar Shatil]

External Email - Use Caution

Hello Doug:


My dti_recon is getting stuck at the "Fitting Tensor" stage. I was wondering if 
there is any solution to the problem "MatrixReadTxT: could not scan value 
[1][1]". My log file is attached here and the problem can be found right at the 
bottom. Is this a bug? What is the solution?


There were similar reports on this earlier but nobody answered.


https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+%5C%5D+dt_recon%22&o=newest&f=1


I am using FS 6.0 in MacOS.


Best,


Anwar


dt_recon.log
Description: dt_recon.log
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Re: [Freesurfer] How to combine and divide surface-based fMRI data?

[Zhi Li]

External Email - Use Caution

Hi Dougles,

Thank your for your reply. Now I am using FSFAST, but I didn't find flags
in prepro-sess which can be used in combing or dividing fMRI data. Using
the following code I could get three files for each run (left cortical
surface, right cortical surface and sub-cortical volume):

*preproc-sess -sf subjects -fsd task_name -sliceorder so -surface fsaverage
lhrh -mni305 -fwhm 5 -per-session*

Can I use preproc-sess to combine files from different runs, and discard
the first 4 time points of each run? If so, could you please give me a
example?

Thanks and best,

Zhi


On Wed, 7 Nov 2018 at 10:16, Greve, Douglas N.,Ph.D. 
wrote:

> Are you using FSFAST? If you run the  preprocessing (preproc-sess), then
> it will get you most of the way there.
>
> On 11/05/2018 10:16 AM, Zhi Li wrote:
> >
> > External Email - Use Caution
> >
> > Hello FreeSurfer experts,
> >
> > May I ask how can I modify the surface-based fMRI data, such as
> > combing two independent sessions into one or dividing one 4D into a
> > series of 3D surface-based fMRI files in which each one denotes a
> > single volume/TR? Thank you very much.
> >
> > Best wishes,
> >
> > Zhi
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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Re: [Freesurfer] How to combine and divide surface-based fMRI data?

[Greve, Douglas N.,Ph.D.]

If you just want to concatenate you can use something like
mri_concat 001/fmcpr.up.sm5.fsaverage.lh.nii.gz 
002/fmcpr.up.sm5.fsaverage.lh.nii.gz 
003/fmcpr.up.sm5.fsaverage.lh.nii.gz --o 
all.fmcpr.up.sm5.fsaverage.lh.nii.gz




On 11/07/2018 12:30 PM, Zhi Li wrote:
>
> External Email - Use Caution
>
> Hi Dougles,
>
> Thank your for your reply. Now I am using FSFAST, but I didn't find 
> flags in prepro-sess which can be used in combing or dividing fMRI 
> data. Using the following code I could get three files for each run 
> (left cortical surface, right cortical surface and sub-cortical volume):
>
> /preproc-sess -sf subjects -fsd task_name -sliceorder so -surface 
> fsaverage lhrh -mni305 -fwhm 5 -per-session/
>
> Can I use preproc-sess to combine files from different runs, and 
> discard the first 4 time points of each run? If so, could you please 
> give me a example?
>
> Thanks and best,
>
> Zhi
>
>
> On Wed, 7 Nov 2018 at 10:16, Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> Are you using FSFAST? If you run the  preprocessing
> (preproc-sess), then
> it will get you most of the way there.
>
> On 11/05/2018 10:16 AM, Zhi Li wrote:
> >
> > External Email - Use Caution
> >
> > Hello FreeSurfer experts,
> >
> > May I ask how can I modify the surface-based fMRI data, such as
> > combing two independent sessions into one or dividing one 4D into a
> > series of 3D surface-based fMRI files in which each one denotes a
> > single volume/TR? Thank you very much.
> >
> > Best wishes,
> >
> > Zhi
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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>
>
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Re: [Freesurfer] GLM

[Greve, Douglas N.,Ph.D.]

Sounds like you need an F-test, eg, create a contrast like
1 1 -1 -1  0  0 0 0 0 0 0 0
1 1  0  0 -1 -1 0 0 0 0 0 0

This tests the null hypothesis that p1==p2==control



On 11/07/2018 10:11 AM, 13181786167 wrote:
>
> External Email - Use Caution
>
> Thanks for your reply. Using the first one, We can obtain the sig.mgh 
> among 3 groups. If I want to obtain the results simultaneously between 
> patient 1 and 2, patient 1 and control, patient 2 and control. What 
> should I do.
>
> Sincerely,
> Zheng
>
>
>
>   
> 郑凤莲
> 邮箱：13181786...@163.com
>
> 
>  
>
>
> 签名由 网易邮箱大师  
> 定制
>
> On 11/07/2018 22:57, Greve, Douglas N.,Ph.D.
>  wrote:
> Use the first one. Not sure what you mean by your multiple
> comparisons
> question
>
> On 11/01/2018 11:20 PM, 郑凤莲 wrote:
> >
> > External Email - Use Caution
> >
> > Hi experts,
> >
> > I am using FS 6.0 for analyzing the cortical thickness
> difference
> > between 3 groups: patient1, patient2 and control. In DODS
> model, I
> > need to creat 2 files, FSDG and mtx file. And we have
> 3 variables:
> > age, gender and cortical thickness.
> > 1. The FSDG file is:
> > GroupDescriptorFile 1
> > Title Tutorial
> > Class patient1-male
> > Class patient1-female
> > Class patient2-male
> > Class patient2-female
> > Class control-male
> > Class control-female
> > Variables                                 age
> > Input subject1 patient1-female 20
> > Input subject2 patient1-male    33
> > Input subject3 patient2-female 40
> > Input subject4 patient2-male    50
> > Input subject5 control-male    30
> > Input subject6 control-female 35
> > And there is another way:
> > GroupDescriptorFile 1
> > Title Tutorial
> > Class patient1
> > Class patient2
> > Class control
> > Variables                     sex age
> > Input subject1 patient1 1   20
> > Input subject2 patient1 2   33
> > Input subject3 patient2 1   40
> > Input subject4 patient2 2   50
> > Input subject5 control   2   30
> > Input subject6 control   1   35
> > What I want to confirm is that if I want to adjust for sex
> and age,
> > which one is right?
> > Another question is that is there any way to get the multiple
> > comparisons between groups simultaneously?
> > I am looking forward to your reply. Thanks very much.
> >
> > Sincerely,
> > Zheng
> >
> >
> >
> >
> > ___
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>
>
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Re: [Freesurfer] MatrixReadTxT: could not scan value [1][1]

[Greve, Douglas N.,Ph.D.]

It is probably trying to use a default bval and bvec file, but it can't 
find it. If you have your bvals and bvects, try passing them explicitly 
to dt_recon

On 11/07/2018 11:56 AM, Anwar Shatil wrote:
>
> External Email - Use Caution
>
> Hello Doug:
>
>
> My dti_recon is getting stuck at the "Fitting Tensor" stage. I was 
> wondering if there is any solution to the problem "MatrixReadTxT: 
> could not scan value [1][1]". My log file is attached here and the 
> problem can be found right at the bottom. Is this a bug? What is the 
> solution?
>
>
> There were similar reports on this earlier but nobody answered.
>
>
> https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+%5C%5D+dt_recon%22&o=newest&f=1
>
>
> I am using FS 6.0 in MacOS.
>
>
> Best,
>
>
> Anwar
>
>
>
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Re: [Freesurfer] mris_apply_reg failing for area/volume

[Greve, Douglas N.,Ph.D.]

Can you send the terminal output that includes the error?

On 11/06/2018 06:36 PM, James Michael Roe wrote:
>  External Email - Use Caution
>
> Hi Bruce
>
> I realise that my last message made it sound as though the problem was fixed.
> However, I was only confirming that the files load fine in freeview (are not 
> corrupted) as asked.
> The issue of many subs area and volume files failing to register when using 
> --jac is still unsolved
>
> Appreciate the support.
>
> Thanks
>
> James
>
> 
> From: James Michael Roe
> Sent: 31 October 2018 19:45
> To: Freesurfer support list
> Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume
>
> Hi Bruce
>
> Can confirm that both files (rh.area & rh.volume) load fine in freeview
>
> Thanks for the help!
>
> James
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Bruce Fischl 
> 
> Sent: 29 October 2018 15:43
> To: Freesurfer support list
> Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume
>
> Hi James
>
> can you verify that the various files (e.g.
> /cluster/projects/p23/projects/Memory_Project/James/AgeSym/long_recons_FXhemi/010_NDev/1000409_02_10_02_11.long.base_1000409_11/surf/rh.area)
>
> are intact by loading them into freeview? For the area file you will of
> course have to load it as an overlay not as a surface (since it isn't a
> surface)
>
> cheers
> Bruce
> On Mon, 29 Oct 2018, James Michael Roe wrote:
>
>>  External Email - Use Caution
>>
>>
>> ​Dear freesurfer experts
>>
>>
>>
>> I’m running the following commands to register RH area and volume files per 
>> sub to both hemispheres
>> of a symmetrical template following Xhemi routines.
>>
>> The commands have already worked for many subs, but are failing to write the 
>> target file for a
>> number of others (and all run fine without the –-jac flag)
>>
>>
>> #right to left
>>
>> mris_apply_reg \
>>
>> --src $SUBJECTS_DIR/$sub/surf/rh.area \
>>
>> --trg $concatdir/rh.lh.area.${sub}.${template}.nii.gz \
>>
>> --streg $SUBJECTS_DIR/$sub/xhemi/surf/lh.${template}.sphere.reg
>> $SUBJECTS_DIR/${template}/surf/lh.sphere.reg \
>>
>> --jac
>>
>>
>>
>> #right to right
>>
>> mris_apply_reg \
>>
>> --src $SUBJECTS_DIR/$sub/surf/rh.area \
>>
>> --trg $concatdir/rh.rh.area.${sub}.${template}.nii.gz \
>>
>> --streg $SUBJECTS_DIR/$sub/surf/rh.${template}.sphere.reg
>> $SUBJECTS_DIR/${template}/surf/rh.sphere.reg \
>>
>> --jac
>>
>>
>>
>>
>> The error is not template-specific as the output is the same using 
>> fsaverage_sym
>>
>> Attached is the log file.
>>
>>
>>
>> Thanks in advance!
>>
>>
>>
>>
>> ​- James
>>
>>
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Re: [Freesurfer] How to combine and divide surface-based fMRI data?

[Zhi Li]

External Email - Use Caution

How can I discard the first 4 time points of each run during concatenating
several runs? I know I can skip the first 4 time points with the flag *-nskip
4* in configuring a analysis, but this condition can be only applicable
when each run is modelled into the GLM independently, right? If I feed the
*mkanalysis-sess* with the concatenated file, it will only skip the first 4
time points of the 1st run in this file.

In addition, if my task design is event-related, do I need to set the
duration of each stimulus as 0?

Thanks and best


On Wed, 7 Nov 2018 at 12:59, Greve, Douglas N.,Ph.D. 
wrote:

>
> If you just want to concatenate you can use something like
> mri_concat 001/fmcpr.up.sm5.fsaverage.lh.nii.gz
> 002/fmcpr.up.sm5.fsaverage.lh.nii.gz
> 003/fmcpr.up.sm5.fsaverage.lh.nii.gz --o
> all.fmcpr.up.sm5.fsaverage.lh.nii.gz
>
>
>
>
> On 11/07/2018 12:30 PM, Zhi Li wrote:
> >
> > External Email - Use Caution
> >
> > Hi Dougles,
> >
> > Thank your for your reply. Now I am using FSFAST, but I didn't find
> > flags in prepro-sess which can be used in combing or dividing fMRI
> > data. Using the following code I could get three files for each run
> > (left cortical surface, right cortical surface and sub-cortical volume):
> >
> > /preproc-sess -sf subjects -fsd task_name -sliceorder so -surface
> > fsaverage lhrh -mni305 -fwhm 5 -per-session/
> >
> > Can I use preproc-sess to combine files from different runs, and
> > discard the first 4 time points of each run? If so, could you please
> > give me a example?
> >
> > Thanks and best,
> >
> > Zhi
> >
> >
> > On Wed, 7 Nov 2018 at 10:16, Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > Are you using FSFAST? If you run the  preprocessing
> > (preproc-sess), then
> > it will get you most of the way there.
> >
> > On 11/05/2018 10:16 AM, Zhi Li wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Hello FreeSurfer experts,
> > >
> > > May I ask how can I modify the surface-based fMRI data, such as
> > > combing two independent sessions into one or dividing one 4D into a
> > > series of 3D surface-based fMRI files in which each one denotes a
> > > single volume/TR? Thank you very much.
> > >
> > > Best wishes,
> > >
> > > Zhi
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu  Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
> > ___
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>
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Re: [Freesurfer] How to combine and divide surface-based fMRI data?

[Greve, Douglas N.,Ph.D.]

First run
mri_convert --nskip 4 
fmcpr.up.sm5.fsaverage.lh.nii.gzfmcpr.up.sm5.fsaverage.lh.skip4.nii.gz
then concat the skip files


On 11/07/2018 01:42 PM, Zhi Li wrote:
>
> External Email - Use Caution
>
> How can I discard the first 4 time points of each run during 
> concatenating several runs? I know I can skip the first 4 time points 
> with the flag /-nskip 4/ in configuring a analysis, but this condition 
> can be only applicable when each run is modelled into the GLM 
> independently, right? If I feed the /mkanalysis-sess/ with the 
> concatenated file, it will only skip the first 4 time points of the 
> 1st run in this file.
>
> In addition, if my task design is event-related, do I need to set the 
> duration of each stimulus as 0?
>
> Thanks and best
>
> On Wed, 7 Nov 2018 at 12:59, Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
>
> If you just want to concatenate you can use something like
> mri_concat 001/fmcpr.up.sm5.fsaverage.lh.nii.gz
> 002/fmcpr.up.sm5.fsaverage.lh.nii.gz
> 003/fmcpr.up.sm5.fsaverage.lh.nii.gz --o
> all.fmcpr.up.sm5.fsaverage.lh.nii.gz
>
>
>
>
> On 11/07/2018 12:30 PM, Zhi Li wrote:
> >
> > External Email - Use Caution
> >
> > Hi Dougles,
> >
> > Thank your for your reply. Now I am using FSFAST, but I didn't find
> > flags in prepro-sess which can be used in combing or dividing fMRI
> > data. Using the following code I could get three files for each run
> > (left cortical surface, right cortical surface and sub-cortical
> volume):
> >
> > /preproc-sess -sf subjects -fsd task_name -sliceorder so -surface
> > fsaverage lhrh -mni305 -fwhm 5 -per-session/
> >
> > Can I use preproc-sess to combine files from different runs, and
> > discard the first 4 time points of each run? If so, could you
> please
> > give me a example?
> >
> > Thanks and best,
> >
> > Zhi
> >
> >
> > On Wed, 7 Nov 2018 at 10:16, Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>
> >>
> wrote:
> >
> >     Are you using FSFAST? If you run the  preprocessing
> >     (preproc-sess), then
> >     it will get you most of the way there.
> >
> >     On 11/05/2018 10:16 AM, Zhi Li wrote:
> >     >
> >     > External Email - Use Caution
> >     >
> >     > Hello FreeSurfer experts,
> >     >
> >     > May I ask how can I modify the surface-based fMRI data,
> such as
> >     > combing two independent sessions into one or dividing one
> 4D into a
> >     > series of 3D surface-based fMRI files in which each one
> denotes a
> >     > single volume/TR? Thank you very much.
> >     >
> >     > Best wishes,
> >     >
> >     > Zhi
> >     >
> >     >
> >     > ___
> >     > Freesurfer mailing list
> >     > Freesurfer@nmr.mgh.harvard.edu
> 
> >      >
> >     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >     ___
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> > Freesurfer@nmr.mgh.harvard.edu
> 
>  >
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
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> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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Re: [Freesurfer] How to combine and divide surface-based fMRI data?

[Zhi Li]

External Email - Use Caution

Great! So I also need to subtract 8 seconds from the onset time of each
stimulus when I make the *paradigm file*, right? If the duration of
stimulus is smaller than 1 second, such as 0.05 second, do I need to change
its duration to 0 in a event-related deign?


On Wed, 7 Nov 2018 at 13:51, Greve, Douglas N.,Ph.D. 
wrote:

> First run
> mri_convert --nskip 4
> fmcpr.up.sm5.fsaverage.lh.nii.gzfmcpr.up.sm5.fsaverage.lh.skip4.nii.gz
> then concat the skip files
>
>
> On 11/07/2018 01:42 PM, Zhi Li wrote:
> >
> > External Email - Use Caution
> >
> > How can I discard the first 4 time points of each run during
> > concatenating several runs? I know I can skip the first 4 time points
> > with the flag /-nskip 4/ in configuring a analysis, but this condition
> > can be only applicable when each run is modelled into the GLM
> > independently, right? If I feed the /mkanalysis-sess/ with the
> > concatenated file, it will only skip the first 4 time points of the
> > 1st run in this file.
> >
> > In addition, if my task design is event-related, do I need to set the
> > duration of each stimulus as 0?
> >
> > Thanks and best
> >
> > On Wed, 7 Nov 2018 at 12:59, Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> >
> > If you just want to concatenate you can use something like
> > mri_concat 001/fmcpr.up.sm5.fsaverage.lh.nii.gz
> > 002/fmcpr.up.sm5.fsaverage.lh.nii.gz
> > 003/fmcpr.up.sm5.fsaverage.lh.nii.gz --o
> > all.fmcpr.up.sm5.fsaverage.lh.nii.gz
> >
> >
> >
> >
> > On 11/07/2018 12:30 PM, Zhi Li wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Hi Dougles,
> > >
> > > Thank your for your reply. Now I am using FSFAST, but I didn't find
> > > flags in prepro-sess which can be used in combing or dividing fMRI
> > > data. Using the following code I could get three files for each run
> > > (left cortical surface, right cortical surface and sub-cortical
> > volume):
> > >
> > > /preproc-sess -sf subjects -fsd task_name -sliceorder so -surface
> > > fsaverage lhrh -mni305 -fwhm 5 -per-session/
> > >
> > > Can I use preproc-sess to combine files from different runs, and
> > > discard the first 4 time points of each run? If so, could you
> > please
> > > give me a example?
> > >
> > > Thanks and best,
> > >
> > > Zhi
> > >
> > >
> > > On Wed, 7 Nov 2018 at 10:16, Greve, Douglas N.,Ph.D.
> > > mailto:dgr...@mgh.harvard.edu>
> > >>
> > wrote:
> > >
> > > Are you using FSFAST? If you run the  preprocessing
> > > (preproc-sess), then
> > > it will get you most of the way there.
> > >
> > > On 11/05/2018 10:16 AM, Zhi Li wrote:
> > > >
> > > > External Email - Use Caution
> > > >
> > > > Hello FreeSurfer experts,
> > > >
> > > > May I ask how can I modify the surface-based fMRI data,
> > such as
> > > > combing two independent sessions into one or dividing one
> > 4D into a
> > > > series of 3D surface-based fMRI files in which each one
> > denotes a
> > > > single volume/TR? Thank you very much.
> > > >
> > > > Best wishes,
> > > >
> > > > Zhi
> > > >
> > > >
> > > > ___
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > >  > >
> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> >  > >
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer ma

Re: [Freesurfer] How to combine and divide surface-based fMRI data?

[Greve, Douglas N.,Ph.D.]

are you trying to use FSFAST to do the entire fmri anlaysis? If so, then 
follow the tutorial as it will handle the skipped TRs and the 
concatenation for you. If not, then you don't need a paradigm file

On 11/07/2018 02:14 PM, Zhi Li wrote:
>
> External Email - Use Caution
>
> Great! So I also need to subtract 8 seconds from the onset time of 
> each stimulus when I make the /paradigm file/, right? If the duration 
> of stimulus is smaller than 1 second, such as 0.05 second, do I need 
> to change its duration to 0 in a event-related deign?
>
>
> On Wed, 7 Nov 2018 at 13:51, Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> First run
> mri_convert --nskip 4
> fmcpr.up.sm5.fsaverage.lh.nii.gzfmcpr.up.sm5.fsaverage.lh.skip4.nii.gz
> then concat the skip files
>
>
> On 11/07/2018 01:42 PM, Zhi Li wrote:
> >
> > External Email - Use Caution
> >
> > How can I discard the first 4 time points of each run during
> > concatenating several runs? I know I can skip the first 4 time
> points
> > with the flag /-nskip 4/ in configuring a analysis, but this
> condition
> > can be only applicable when each run is modelled into the GLM
> > independently, right? If I feed the /mkanalysis-sess/ with the
> > concatenated file, it will only skip the first 4 time points of the
> > 1st run in this file.
> >
> > In addition, if my task design is event-related, do I need to
> set the
> > duration of each stimulus as 0?
> >
> > Thanks and best
> >
> > On Wed, 7 Nov 2018 at 12:59, Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>
> >>
> wrote:
> >
> >
> >     If you just want to concatenate you can use something like
> >     mri_concat 001/fmcpr.up.sm5.fsaverage.lh.nii.gz
> >     002/fmcpr.up.sm5.fsaverage.lh.nii.gz
> >     003/fmcpr.up.sm5.fsaverage.lh.nii.gz --o
> >     all.fmcpr.up.sm5.fsaverage.lh.nii.gz
> >
> >
> >
> >
> >     On 11/07/2018 12:30 PM, Zhi Li wrote:
> >     >
> >     > External Email - Use Caution
> >     >
> >     > Hi Dougles,
> >     >
> >     > Thank your for your reply. Now I am using FSFAST, but I
> didn't find
> >     > flags in prepro-sess which can be used in combing or
> dividing fMRI
> >     > data. Using the following code I could get three files for
> each run
> >     > (left cortical surface, right cortical surface and
> sub-cortical
> >     volume):
> >     >
> >     > /preproc-sess -sf subjects -fsd task_name -sliceorder so
> -surface
> >     > fsaverage lhrh -mni305 -fwhm 5 -per-session/
> >     >
> >     > Can I use preproc-sess to combine files from different
> runs, and
> >     > discard the first 4 time points of each run? If so, could you
> >     please
> >     > give me a example?
> >     >
> >     > Thanks and best,
> >     >
> >     > Zhi
> >     >
> >     >
> >     > On Wed, 7 Nov 2018 at 10:16, Greve, Douglas N.,Ph.D.
> >     > mailto:dgr...@mgh.harvard.edu>
> >
> >         >     wrote:
> >     >
> >     >     Are you using FSFAST? If you run the preprocessing
> >     >     (preproc-sess), then
> >     >     it will get you most of the way there.
> >     >
> >     >     On 11/05/2018 10:16 AM, Zhi Li wrote:
> >     >     >
> >     >     > External Email - Use Caution
> >     >     >
> >     >     > Hello FreeSurfer experts,
> >     >     >
> >     >     > May I ask how can I modify the surface-based fMRI data,
> >     such as
> >     >     > combing two independent sessions into one or
> dividing one
> >     4D into a
> >     >     > series of 3D surface-based fMRI files in which each one
> >     denotes a
> >     >     > single volume/TR? Thank you very much.
> >     >     >
> >     >     > Best wishes,
> >     >     >
> >     >     > Zhi
> >     >     >
> >     >     >
> >     >     > ___
> >     >     > Freesurfer mailing list
> >     >     > Freesurfer@nmr.mgh.harvard.edu
> 
> >      >
> >     >      
> >      >>
> >     >     >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >     >
>

Re: [Freesurfer] How to combine and divide surface-based fMRI data?

[Zhi Li]

External Email - Use Caution

I see. Thank you very much.

On Wed, 7 Nov 2018 at 15:18, Greve, Douglas N.,Ph.D. 
wrote:

> are you trying to use FSFAST to do the entire fmri anlaysis? If so, then
> follow the tutorial as it will handle the skipped TRs and the
> concatenation for you. If not, then you don't need a paradigm file
>
> On 11/07/2018 02:14 PM, Zhi Li wrote:
> >
> > External Email - Use Caution
> >
> > Great! So I also need to subtract 8 seconds from the onset time of
> > each stimulus when I make the /paradigm file/, right? If the duration
> > of stimulus is smaller than 1 second, such as 0.05 second, do I need
> > to change its duration to 0 in a event-related deign?
> >
> >
> > On Wed, 7 Nov 2018 at 13:51, Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > First run
> > mri_convert --nskip 4
> >
>  fmcpr.up.sm5.fsaverage.lh.nii.gzfmcpr.up.sm5.fsaverage.lh.skip4.nii.gz
> > then concat the skip files
> >
> >
> > On 11/07/2018 01:42 PM, Zhi Li wrote:
> > >
> > > External Email - Use Caution
> > >
> > > How can I discard the first 4 time points of each run during
> > > concatenating several runs? I know I can skip the first 4 time
> > points
> > > with the flag /-nskip 4/ in configuring a analysis, but this
> > condition
> > > can be only applicable when each run is modelled into the GLM
> > > independently, right? If I feed the /mkanalysis-sess/ with the
> > > concatenated file, it will only skip the first 4 time points of the
> > > 1st run in this file.
> > >
> > > In addition, if my task design is event-related, do I need to
> > set the
> > > duration of each stimulus as 0?
> > >
> > > Thanks and best
> > >
> > > On Wed, 7 Nov 2018 at 12:59, Greve, Douglas N.,Ph.D.
> > > mailto:dgr...@mgh.harvard.edu>
> > >>
> > wrote:
> > >
> > >
> > > If you just want to concatenate you can use something like
> > > mri_concat 001/fmcpr.up.sm5.fsaverage.lh.nii.gz
> > > 002/fmcpr.up.sm5.fsaverage.lh.nii.gz
> > > 003/fmcpr.up.sm5.fsaverage.lh.nii.gz --o
> > > all.fmcpr.up.sm5.fsaverage.lh.nii.gz
> > >
> > >
> > >
> > >
> > > On 11/07/2018 12:30 PM, Zhi Li wrote:
> > > >
> > > > External Email - Use Caution
> > > >
> > > > Hi Dougles,
> > > >
> > > > Thank your for your reply. Now I am using FSFAST, but I
> > didn't find
> > > > flags in prepro-sess which can be used in combing or
> > dividing fMRI
> > > > data. Using the following code I could get three files for
> > each run
> > > > (left cortical surface, right cortical surface and
> > sub-cortical
> > > volume):
> > > >
> > > > /preproc-sess -sf subjects -fsd task_name -sliceorder so
> > -surface
> > > > fsaverage lhrh -mni305 -fwhm 5 -per-session/
> > > >
> > > > Can I use preproc-sess to combine files from different
> > runs, and
> > > > discard the first 4 time points of each run? If so, could you
> > > please
> > > > give me a example?
> > > >
> > > > Thanks and best,
> > > >
> > > > Zhi
> > > >
> > > >
> > > > On Wed, 7 Nov 2018 at 10:16, Greve, Douglas N.,Ph.D.
> > > > mailto:dgr...@mgh.harvard.edu>
> > >
> > >  >   >  > > wrote:
> > > >
> > > > Are you using FSFAST? If you run the preprocessing
> > > > (preproc-sess), then
> > > > it will get you most of the way there.
> > > >
> > > > On 11/05/2018 10:16 AM, Zhi Li wrote:
> > > > >
> > > > > External Email - Use Caution
> > > > >
> > > > > Hello FreeSurfer experts,
> > > > >
> > > > > May I ask how can I modify the surface-based fMRI data,
> > > such as
> > > > > combing two independent sessions into one or
> > dividing one
> > > 4D into a
> > > > > series of 3D surface-based fMRI files in which each one
> > > denotes a
> > > > > single volume/TR? Thank you very much.
> > > > >
> > > > > Best wishes,
> > > > >
> > > > > Zhi
> > > > >
> > > > >
> > > > > ___
> > > > > Freesurfer mailing list
> > > > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > > 

[Freesurfer] Desikian-Killiany and Destrieux atlas

[Miguel Ángel Rivas Fernández]

External Email - Use Caution

Hello Freesurfer devs,


Is there available any Desikian-Killiany and Destrieux atlas template or
image downloadable with all brain labels of the atlas? I would to use this
image to show my results in a lab meeting? I would need somethig similar
that the lookup table used in the freeview.


Cheers,

-- 
*Miguel Ángel Rivas Fernández*
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Re: [Freesurfer] Desikian-Killiany and Destrieux atlas

[Bruce Fischl]

Hi Miguel

I think we distribute parcellations of the fsaverage subject (and of bert 
and ernie), so if you have any of those you can use them to show the 
atlas labels. The atlases themselves are more complicated and store other 
information that isn't easily visualizable


cheers
Bruce
On Wed, 7 Nov 2018, Miguel Ángel 
Rivas Fernández wrote:




External Email - Use Caution


Hello Freesurfer devs,


Is there available any Desikian-Killiany and Destrieux atlas template or image 
downloadable with all
brain labels of the atlas? I would to use this image to show my results in a 
lab meeting? I would
need somethig similar that the lookup table used in the freeview.


Cheers,

--
Miguel Ángel Rivas Fernández

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Re: [Freesurfer] Desikian-Killiany and Destrieux atlas

[Greve, Douglas N.,Ph.D.]

I'm not sure what you mean. The atlas is distributed with FS.

On 11/07/2018 05:09 PM, Miguel Ángel Rivas Fernández wrote:
>
> External Email - Use Caution
>
>
> Hello Freesurfer devs,
>
>
> Is there available any Desikian-Killiany and Destrieux atlas template 
> or image downloadable with all brain labels of the atlas? I would to 
> use this image to show my results in a lab meeting? I would need 
> somethig similar that the lookup table used in the freeview.
>
>
> Cheers,
>
> -- 
> *Miguel Ángel Rivas Fernández*
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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[Freesurfer] dcmunpack Error

[Maryam Tayebi]

External Email - Use Caution

Hello Freesurfer Developers,
I was going to reconstruct MPRAGE images from GE 3T machine.
First I used this command:
*dcmunpack -src . -scanonly scan.log*

It made just *scan.log* file for me. Then I used this command:
*unpacksdcmdir -src / -targ 
-scanonly scan.log*

However, it made 3 files for me; dicomdir.sumfile, parse.status and
unpack.log, but they were 0 bites. Furthermore, the following message also
appeared on the terminal:


*ERROR: parsing /hpc/mtay316/tutorial4/practice_with_data/dicoms/ See
logfile /hpc/mtay316/tutorial4/practice_with_data//unpack.log for more
details*

I used this command for SIEMENS data and it worked. Apparently this code
just works on SIEMENS data not GE. So now what is the code that I can use
for GE dcm images?

1) FREESURFER Version: freesurfer-x86_64-unknown-linux-gnu-stable6-20170118
2) Platform: Ubuntu 16.04 LTS
3) unpack.log : see attached

Regards


-- 
*Maryam Tayebi*

PhD Candidate of Bioengineering
Auckland Bioengineering Institute, University of Auckland, Auckland, New
Zealand



MSc of Medical Imaging
University of Manchester, Manchester, UK
Log file created by unpacksdcmdir
$Id: unpacksdcmdir,v 1.25 2015/02/06 19:19:50 greve Exp $
/hpc/mtay316/tutorial4/practice_with_data//unpack.log
/hpc_htom/mtay316/tutorial4/practice_with_data/dicoms
Thu Nov  8 10:59:10 NZDT 2018
-src /hpc/mtay316/tutorial4/practice_with_data/dicoms/ -targ /hpc/mtay316/tutorial4/practice_with_data/ -scanonly scan.log
mri_convert.bin -all-info 
ProgramName: mri_convert.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/11/07-21:59:10-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: mtay316  Machine: bn390370  Platform: Linux  PlatformVersion: 4.15.0-36-generic  CompilerName: GCC  CompilerVersion: 40400 
bn390370
Linux bn390370 4.15.0-36-generic #39~16.04.1-Ubuntu SMP Tue Sep 25 08:59:23 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
SkipMoCo 0
dicomdir /hpc/mtay316/tutorial4/practice_with_data/dicoms/
Scanning source directory ...
INFO: summary file is /hpc/mtay316/tutorial4/practice_with_data//dicomdir.sumfile
INFO: status file is /hpc/mtay316/tutorial4/practice_with_data//parse.status
mri_parse_sdcmdir --sortbyrun --d /hpc/mtay316/tutorial4/practice_with_data/dicoms/ --o /hpc/mtay316/tutorial4/practice_with_data//dicomdir.sumfile --status /hpc/mtay316/tutorial4/practice_with_data//parse.status
INFO: scanning path to Siemens DICOM DIR:
   /hpc/mtay316/tutorial4/practice_with_data/dicoms
INFO: Found 175 files in /hpc/mtay316/tutorial4/practice_with_data/dicoms
INFO: counting Siemens Files
$Id: mri_parse_sdcmdir.c,v 1.22 2015/05/21 16:37:12 greve Exp $
cwd /hpc_htom/mtay316/tutorial4/practice_with_data/dicoms
cmdline --sortbyrun --d /hpc/mtay316/tutorial4/practice_with_data/dicoms/ --o /hpc/mtay316/tutorial4/practice_with_data//dicomdir.sumfile --status /hpc/mtay316/tutorial4/practice_with_data//parse.status 
sysname  Linux
hostname bn390370
machine  x86_64
user mtay316
INFO: found 0 Siemens Files
ERROR: scanning directory /hpc/mtay316/tutorial4/practice_with_data/dicoms
ERROR: parsing /hpc/mtay316/tutorial4/practice_with_data/dicoms/ 
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Re: [Freesurfer] T-value in QDEC or FREESURFER

[Greve, Douglas N.,Ph.D.]

On 11/03/2018 02:20 AM, Vikas Bandalli wrote:
>
> External Email - Use Caution
>
> Dear  freesurfer team.
>
> I am running an analysis betweene two groups Normal and Patients.
> Here is an example of my particular design
> diagnosis :- Normal vs Bipolar
> Co-variate :- Age
> Nuisance factor :- Total_Intra cranial volume
>
> I would please like to know a couple of things related to QDEC
> 1.I am looking for difference in volume between patients and controls 
> and the analysis. For correcting for multiple comparisons I ran Monte 
> carlo - Z simulation at threshold of 1.3
> My understanding is the analysis overall runs a two-tailed t-test 
> first and then when we select to run MC-z simulation it iterates for 
> multiple comparisions (by repeating the saem say 1000 times ) and 
> gives out 'clusterwise p-value'
> Is my understanding correct?
It synthesizes a z-field, then smoothes it based on the smoothness of 
the residual of the real data, then thresholds, finds the max cluster 
size. It then repeats 1000 times. It then computes the p-value of your 
cluster based on the number of times it saw a cluster of the same size 
or bigger out of the 1000 trials. Note: for a threshold of 1.3, we 
recommend that you do permutation instead since the cluster p-value is 
very liberal using the MCZ simulation.
>
> 2.I would like to extract T-values for the same . Are we getting 
> cluster wise T-value similar to cluster wise p-value ?
> in the terminal
The cluster pvalue is not based on a t-test. You can get t-value from 
the original voxel-wise analysis. Look in the output folder under each 
contrast. You will find F.mgh and gamma.mgh. t = sign(gamma)*sqrt(F) 
(assuming it is a t-contrast and not an F)
>
> 3. Where would I find t-values for the analysis ???
See above
>
> 4.Are there any methods to extract T-values in qdec or freesurfer . If 
> so,please specify.
>
> I am enclosing screenshots from my analysis for the same . Kindly 
> request you to please have a look please help me out with this ??
>
> Thanking You,
>
> Yours sincerely ,
> Dr.Vikas Bandalli
>
> --
> Bangalore Medical College and Research Institute (BMCRI),
> Bangalore,India,
> Ph : +918904286825


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Re: [Freesurfer] dcmunpack Error

[Greve, Douglas N.,Ph.D.]

You have to specify an output directory with -targ and the runs you want 
to unpack with -run. See the help (ie, run dcmunpack with -help)

On 11/07/2018 05:38 PM, Maryam Tayebi wrote:
>
> External Email - Use Caution
>
> Hello Freesurfer Developers,
> I was going to reconstruct MPRAGE images from GE 3T machine.
> First I used this command:
> /dcmunpack -src . -scanonly scan.log/
>
> It made just /scan.log/ file for me. Then I used this command:
> /unpacksdcmdir -src / -targ  
> -scanonly scan.log/
>
> However, it made 3 files for me; dicomdir.sumfile, parse.status and 
> unpack.log, but they were 0 bites. Furthermore, the following message 
> also appeared on the terminal:
>
> /ERROR: parsing /hpc/mtay316/tutorial4/practice_with_data/dicoms/
> See logfile /hpc/mtay316/tutorial4/practice_with_data//unpack.log for 
> more details/
>
> I used this command for SIEMENS data and it worked. Apparently this 
> code just works on SIEMENS data not GE. So now what is the code that I 
> can use for GE dcm images?
>
> 1) FREESURFER Version: 
> freesurfer-x86_64-unknown-linux-gnu-stable6-20170118
> 2) Platform: Ubuntu 16.04 LTS
> 3) unpack.log : see attached
>
> Regards
>
>
> -- 
> *Maryam Tayebi*
>
> PhD Candidate of Bioengineering
> Auckland Bioengineering Institute, University of Auckland, Auckland, 
> New Zealand
>
>
>
> MSc of Medical Imaging
> University of Manchester, Manchester, UK
>
>
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[Freesurfer] Ventricles segmentation

[Miguel Ángel Rivas Fernández]

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Hello Freesurfer devs,


Is possible segment the brain ventricles using Freesurfer in terms of mm3
or ml? I would be interested in study the ventricular enlargement. Is
possible with Freesurfer or other toolbox.


Any help would be appreciated. Thanks in advance.

Cheers,

-- 
*Miguel Ángel Rivas Fernández*
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Re: [Freesurfer] Ventricles segmentation

[Bruce Fischl]

Hi Miguel,

yes, we report ventricular volume in mm^3 in the stats files.

cheers
Bruce
On Thu, 8 Nov 
2018, Miguel Ángel Rivas Fernández wrote:




External Email - Use Caution


Hello Freesurfer devs,


Is possible segment the brain ventricles using Freesurfer in terms of mm3 or 
ml? I would be
interested in study the ventricular enlargement. Is possible with Freesurfer or 
other toolbox.


Any help would be appreciated. Thanks in advance.

Cheers,

--
Miguel Ángel Rivas Fernández

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[Freesurfer] Basic question in testing installation by 4 examples

[Zainab Albar]

External Email - Use Caution

Hello Freesurfer expert, I am brand new to Freesurfer, my apology for the
basic question, I kept trying to figure out my mistake in installation for
last week and could not find a solution to it.

Here is my output, my problem with subject_DIR keeps changing and recon
command is not found. it worked only once with me till I reach example 4
when I had an output that libpng12.so.0 not found.

Thank you for help in advance,

zhbar@DESKTOP-V43QKHC:~$ export FREESURFER_HOME=/usr/local/freesurfer
zhbar@DESKTOP-V43QKHC:~$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni
zhbar@DESKTOP-V43QKHC:~$ export SUBJECTS_DIR=path to subject data
zhbar@DESKTOP-V43QKHC:~$ sudo cp $FREESURFER_HOME/subjects/sample-001.mgz .
[sudo] password for zhbar:
zhbar@DESKTOP-V43QKHC:~$ mri_convert sample-001.mgz sample-001.nii.gz
mri_convert.bin sample-001.mgz sample-001.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from sample-001.mgz...
TR=7.25, TE=3.22, TI=600.00, flip angle=7.00
i_ras = (-0, -1, -0)
j_ras = (-0, 0, -1)
k_ras = (-1, 0, 0)
writing to sample-001.nii.gz...
zhbar@DESKTOP-V43QKHC:~$ export SUBJECTS_DIR=path to subject directory
zhbar@DESKTOP-V43QKHC:~$ recon-all -i sample-001.nii.gz -s bert -all
ERROR: SUBJECTS_DIR path does not exist.
zhbar@DESKTOP-V43QKHC:~$ sudo recon-all -i sample-001.nii.gz -s bert -all
sudo: recon-all: command not found
zhbar@DESKTOP-V43QKHC:~$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
WARNING: path does not exist
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  path
MNI_DIR   /usr/local/freesurfer/mni
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Re: [Freesurfer] dcmunpack Error

[Maryam Tayebi]

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I tried this way, but I got lots of errors, as the attached file. What is
the problem? Is there anything wrong with my data? Because I am using the
online databases which I think it might be back to 2009 ish.

Thanks

On Thu, 8 Nov 2018 at 11:55, Greve, Douglas N.,Ph.D. 
wrote:

> You have to specify an output directory with -targ and the runs you want
> to unpack with -run. See the help (ie, run dcmunpack with -help)
>
> On 11/07/2018 05:38 PM, Maryam Tayebi wrote:
> >
> > External Email - Use Caution
> >
> > Hello Freesurfer Developers,
> > I was going to reconstruct MPRAGE images from GE 3T machine.
> > First I used this command:
> > /dcmunpack -src . -scanonly scan.log/
> >
> > It made just /scan.log/ file for me. Then I used this command:
> > /unpacksdcmdir -src / -targ 
> > -scanonly scan.log/
> >
> > However, it made 3 files for me; dicomdir.sumfile, parse.status and
> > unpack.log, but they were 0 bites. Furthermore, the following message
> > also appeared on the terminal:
> >
> > /ERROR: parsing /hpc/mtay316/tutorial4/practice_with_data/dicoms/
> > See logfile /hpc/mtay316/tutorial4/practice_with_data//unpack.log for
> > more details/
> >
> > I used this command for SIEMENS data and it worked. Apparently this
> > code just works on SIEMENS data not GE. So now what is the code that I
> > can use for GE dcm images?
> >
> > 1) FREESURFER Version:
> > freesurfer-x86_64-unknown-linux-gnu-stable6-20170118
> > 2) Platform: Ubuntu 16.04 LTS
> > 3) unpack.log : see attached
> >
> > Regards
> >
> >
> > --
> > *Maryam Tayebi*
> >
> > PhD Candidate of Bioengineering
> > Auckland Bioengineering Institute, University of Auckland, Auckland,
> > New Zealand
> >
> >
> >
> > MSc of Medical Imaging
> > University of Manchester, Manchester, UK
> >
> >
> > ___
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>
>
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-- 
*Maryam Tayebi*

PhD Candidate of Bioengineering
Auckland Bioengineering Institute, University of Auckland, Auckland, New
Zealand



MSc of Medical Imaging
University of Manchester, Manchester, UK

cd /hpc_htom/mtay316/tutorial4/practice_with_data/Subj01
/hpc/mtay316/freesurfer/bin/dcmunpack -src . -targ /hpc/mtay316/tutorial4/practice_with_data/mprage -run 4 /hpc/mtay316/tutorial4/practice_with_data/Subj01/ nii.gz 1.nii.gz

$Id: dcmunpack,v 1.19.2.1 2016/08/02 21:12:01 greve Exp $
-rwxr-xr-x 1 mtay316 graduate 23759 Jan 19  2017 /hpc/mtay316/freesurfer/bin/dcmunpack
Linux bn390370 4.15.0-36-generic #39~16.04.1-Ubuntu SMP Tue Sep 25 08:59:23 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
Thu Nov  8 15:26:20 NZDT 2018
---
  1 4 /hpc/mtay316/tutorial4/practice_with_data/Subj01/ 1 0 0
---
Searching for matching files
Thu Nov  8 15:26:20 NZDT 2018
Searching .
Thu Nov  8 15:26:20 NZDT 2018
Found 177 total files.
#@# 2/177 Thu Nov  8 15:26:20 NZDT 2018
#@# 3/177 Thu Nov  8 15:26:20 NZDT 2018
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Re: [Freesurfer] Basic question in testing installation by 4 examples

[fsbuild]

External Email - Use Caution

​Hello Zainab,
The first 2 commands you list are,
 export FREESURFER_HOME=/usr/local/freesurfersource 
$FREESURFER_HOME/SetUpFreeSurfer.sh
 and the output from the source command shows you what has been setup in 
your environment...
FREESURFER_HOME   /usr/local/freesurferFSFAST_HOME    
   /usr/local/freesurfer/fsfastFSF_OUTPUT_FORMAT 
nii.gzSUBJECTS_DIR      
/usr/local/freesurfer/subjectsMNI_DIR          
 /usr/local/freesurfer/mni
Now there should be no need to run more export commands, i.e.,  
SUBJECTS_DIR is already set correctly.    But the next export 
command you type,
export SUBJECTS_DIR=path to subject directory
- changed the setting of SUBJECTS_DIR from "/usr/local/freesurfer/subjects" to 
"path to subject directory" which is a path that does not exist

You only need to run the export and source commands once in your current shell 
before runningany/all subsequent freesurfer commands.



Zainab AlbarNovember 7, 2018 at 19:29
  External Email - Use 
CautionHello Freesurfer
 expert, I am brand new to Freesurfer, my apology for the basic 
question, I kept trying to figure out my mistake in installation for 
last week and could not find a solution to it.
Here
 is my output, my problem with subject_DIR keeps changing and recon 
command is not found. it worked only once with me till I reach example 4
 when I had an output that libpng12.so.0 not found.
Thank you for help in advance,
zhbar@DESKTOP-V43QKHC:~$ export 
FREESURFER_HOME=/usr/local/freesurferzhbar@DESKTOP-V43QKHC:~$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Setting up 
environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME  
 /usr/local/freesurferFSFAST_HOME      
 /usr/local/freesurfer/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR  
    /usr/local/freesurfer/subjectsMNI_DIR        
   /usr/local/freesurfer/mnizhbar@DESKTOP-V43QKHC:~$ export 
SUBJECTS_DIR=path to subject datazhbar@DESKTOP-V43QKHC:~$ sudo cp 
$FREESURFER_HOME/subjects/sample-001.mgz .[sudo] password for 
zhbar:zhbar@DESKTOP-V43QKHC:~$ mri_convert sample-001.mgz 
sample-001.nii.gzmri_convert.bin sample-001.mgz sample-001.nii.gz$Id: 
mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from 
sample-001.mgz...TR=7.25, TE=3.22, TI=600.00, flip angle=7.00i_ras = (-0, -1, 
-0)j_ras = (-0, 0, -1)k_ras = (-1, 0, 0)writing to 
sample-001.nii.gz...zhbar@DESKTOP-V43QKHC:~$ export SUBJECTS_DIR=path to 
subject directoryzhbar@DESKTOP-V43QKHC:~$ recon-all -i sample-001.nii.gz -s 
bert -allERROR: SUBJECTS_DIR path does not exist.zhbar@DESKTOP-V43QKHC:~$ sudo 
recon-all -i sample-001.nii.gz -s bert -allsudo: recon-all: command not 
foundzhbar@DESKTOP-V43QKHC:~$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Setting up 
environment for FreeSurfer/FS-FAST (and FSL)WARNING: path does not 
existFREESURFER_HOME   /usr/local/freesurferFSFAST_HOME    
   /usr/local/freesurfer/fsfastFSF_OUTPUT_FORMAT 
nii.gzSUBJECTS_DIR      pathMNI_DIR        
   /usr/local/freesurfer/mni


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[Freesurfer] Cerelellar parcellation labels Request

[dongnandi1]

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Hi Freesurfer experts,

The cerebellar 7 and 17 networks parcellation cannot be downloaded. 

The link to cerebellar parcellation in SUIT is out of date too.



so, if you can kindly share the cerebellar 17-network parcellation and 
their anatomy labels, I would be particularly grateful!

 Best wishes




Fan

2018/11/08___
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