[Freesurfer] mri_surfcluster to obtain ROI (label) centroid MNI coordinates

[Ladan Shahshahani]

Hi,

Following previous discussions on the mailing list, I am using
mri_surfcluster to extract MNI (or Talairach) coordinates of a label using:

mri_surfcluster --in $SUBJECTS_DIR/fsaverage/surf/lh.area --clabel
lh.G_cingulate-Isthmus.label --sum ~/Desktop/pract3 --centroid --thmin 0
--hemi lh --subject fsaverage --nofixmni
I tried different labels, but for all of them I get the following
coordinates (for left hemisphere):
-29.4  -22.0   17.4

I see that others are having the same problem, like the one in the
following link:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2015-November/042446.html

Am I missing something here?
What can I do to solve this problem?

Bests,
Ladan
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[Freesurfer] Error mri_surf2surf FS6

[Juergen Haenggi]

Dear FS experts

we are trying to run statistics in FS6 Linux. Everthing worked fine until we 
applied the command
mris_preproc that called mri_surf2surf and produced the following error:

#

---
#@# 1/98 s1006_01.long.s1006_base Thu Mar  9 13:20:16 CET 2017 --
---
mri_surf2surf --srcsubject s1006_01.long.s1006_base --srchemi rh --srcsurfreg 
average_AN_FS6_long_split.sphere.reg --trgsubject average_AN_FS6_long_split 
--trghemi rh --trgsurfreg sphere.reg --tval 
./average_AN_FS6_long_split/stats/lme_preproc/tmp.mris_preproc.3575/s1006_01.long.s1006_base.1.mgh
 --sval /usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.volume 
--jac --sfmt curv --noreshape --cortex
MRISread(/usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.average_AN_FS6_long_split.sphere.reg):
 could not open file
Source registration surface changed to average_AN_FS6_long_split.sphere.reg
Target registration surface changed to sphere.reg

$Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $

setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
cd /usr/local/freesurfer/subjects
mri_surf2surf --srcsubject s1006_01.long.s1006_base --srchemi rh --srcsurfreg 
average_AN_FS6_long_split.sphere.reg --trgsubject average_AN_FS6_long_split 
--trghemi rh --trgsurfreg sphere.reg --tval 
./average_AN_FS6_long_split/stats/lme_preproc/tmp.mris_preproc.3575/s1006_01.long.s1006_base.1.mgh
 --sval /usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.volume 
--jac --sfmt curv --noreshape --cortex 

sysname  Linux
hostname psy-neuro-clt-Monster
machine  x86_64
user ego
srcsubject = s1006_01.long.s1006_base
srcval = 
/usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.volume
srctype= curv
trgsubject = average_AN_FS6_long_split
trgval = 
./average_AN_FS6_long_split/stats/lme_preproc/tmp.mris_preproc.3575/s1006_01.long.s1006_base.1.mgh
trgtype= 
srcsurfreg = average_AN_FS6_long_split.sphere.reg
trgsurfreg = sphere.reg
srchemi= rh
trghemi= rh
frame  = 0
fwhm-in= 0
fwhm-out   = 0
label-src  = rh.cortex.label
label-trg  = rh.cortex.label
OKToRevFaceOrder  = 1
UseDualHemi = 0
Reading source surface reg 
/usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.average_AN_FS6_long_split.sphere.reg
No such file or directory
mri_surf2surf: could not read surface 
/usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.average_AN_FS6_long_split.sphere.reg
No such file or directory

###

this line is odd:

MRISread(/usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.average_AN_FS6_long_split.sphere.reg):
 could not open file

we are wondering why FS6 introduced the name of the target average 
(average_AN_FS6_long_split) into the name of the individual subject 
(rh.average_AN_FS6_long_split.sphere.reg) when looking for 
s1006_01.long.s1006_base/surf/rh.sphere.reg.

When using FS5.3.0 mris_preproc worked without this error.

Any idea?

Thanks in advance
Best regards
Jürgen


-
University of Zurich
Dr. Jürgen Hänggi, Ph.D.
Department of Psychology
Division Neuropsychology
Binzmuehlestrasse 14, PO Box 25 
8050 Zurich, Switzerland

0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)   
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number) 

j.haen...@psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)   

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Re: [Freesurfer] mri_label2vol error: could not scan # of lines from label file

[Bruce Fischl]

Hi Joshua

hmmm, label2vol takes our text label file format as input, not a .gii 
file. You probably need to ask the Wash U HCP folks how to do this 
conversion as I believe there should be a step before label2vol


cheers
Bruce


On Thu, 9 Mar 2017, 
Burks, Joshua D (HSC) wrote:



Hello FreeSurfer Developers,
I’m attempting to convert a dlabel file from the Human Connectome Project to
a volumetric ROI that I can use for fiber tractography on other platforms. I
followed the tutorial provided by HCP (hcp-users FAQ #9: How do I map data
between FreeSurfer ... - HCP Wiki) for resampling HCP-derived data for use
in FreeSurfer.

When I run the mri_label2vol command:

mri_label2vol: could not scan # of lines from label file
ERROR reading /home/neuroresearch/workbench/test1.label.gii

Does anyone have thoughts on how to troubleshoot this? I have not seen any
similar errors described in the list.

1) FreeSurfer version: freesurfer-x86_64-apple-darwin16.4.0-dev-20170302
2) Platform: MacOS 10.12.3

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Re: [Freesurfer] Results from R to Freesurfer

[Bruce Fischl]

Hi Dorian

that is a bit worriesome. Typically the surfaces are "frozen" at the 
midline and hence the thickness is 0, so there should be no difference. I 
guess if a single subject had an incorrect CC segmentation you would be 0 
variance within one group and hence significant results or something like 
that. We usually mask out the midline also using the ?h.cortex.label file.

As for the parcel question, fsaverage should have .annot files in the label 
dir that correespond to various parcellations. YOu can read them into 
matlab with read_annotation.m

I'll leave the 3rd question for someone else
cheers
Bruce

On Wed, 8 Mar 2017, Dorian P. wrote:

> Hi Freesurfers,
> I am using R to perform thickness analyses. All subjects are transformed in
> fsaverage space and all values are placed in a matrix with 327684 columns
> (163842 for each hemisphere). I put the results back in a surface file (.asc
> format) and then convert it to a binary Freesurfer format. I then open the
> files in Freesurfer to view them.
> 
> Overall the results make sense and fall in the right places. But I am
> concerned that some results fall into the corpus callosum, which, if I
> remember correctly should not have any thickness value, and therefore no
> results.
> 
> Here is a screenshot:
> Inline image 1
> 
> Can someone help my understand what might be wrong? Or, if this is normal,
> why I am finding thickness results where there is no thickness?
> 
> Is there a way to find label numbers for each vertex in fsaverage space
> (i.e. list of parcel number for each vertex). This might be useful to
> exclude certain vertices or compute summery statistics of the results
> directly in R.
> 
> Third question, is it possible to threshold the above map based on minimal
> cluster area (i.e., in mri_surfcluster). If yes, do I need to prepare a
> binary file with p-values for thresholding (0-1), or can I use
> mri_surfcluster with t-score maps (0-Inf)?
> 
> Thank you for your help.
> Dorian
> 
> 
>
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Re: [Freesurfer] mri_concat pet images into 1 template image

[Douglas N Greve]

How are you planning on analyzing the different time points?


On 03/08/2017 05:33 PM, Shane S wrote:
> Dear Doug,
>
> My PET data is 3 x 5 minute acquisitions. Each subject has
> subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz and I am 
> supposed to align and average them.
>
> Please advise.
>
> Thanks!
>
> -- 
> Shane Schofield
>
> On 8 March 2017 at 22:31:06, Douglas Greve (gr...@nmr.mgh.harvard.edu 
> ) wrote:
>
>> No, the template is a within subject template used for registration. 
>> If your pet data only has one frame (eg, FDG SUV), then you don't 
>> need to run mri_convert or mri_concat, just use your pet image as the 
>> template
>>
>>
>> On 3/8/17 11:11 AM, Shane S wrote:
>>> Hello Freesurfer,
>>>
>>> I have 3 PET images per individual. I am learning PetSurfer based on 
>>> the Greve et al., 2014 paper.
>>>
>>> On the PetSurfer link, there are 2 methods.
>>>
>>> mri_convert pet.nii.gz —frame frameno template.nii.gz
>>> or
>>> mri_concat pet.nii.gz --mean —0 template.nii.gz
>>>
>>> What are the differences? My files are listed as 
>>> subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz
>>>
>>> Is "mri_concat subject123_a.nii.gz, subject123_b.nii.gz, 
>>> subject123_c.nii.gz —mean —o template.nii.gz” correct?
>>>
>>> Thank you for helping.
>>>
>>> Best Wishes,
>>>
>>> S
>>> -- 
>>> Shane Schofield
>>>
>>>
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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
>>
>>
>> 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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-- 
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
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Re: [Freesurfer] Issue with mri_segstats to extract cortical thickness from a volume ROI

[Douglas N Greve]

How did you create lh.fsaverage.ROI5.mgh and lh.thickness.fsaverage.mgh?


On 03/08/2017 08:15 PM, Elodie Boudes wrote:
> Hello FreeSurfer community,
>
> I am trying to extract the cortical thickness from a specific ROI.
> I followed the pipeline: cortical thickness of a volume-defined ROI. 
> But for the last step:
> mri_segstats \
>--seg $SUBJECTS_DIR/fsaverage/surf/lh.fsaverage.ROI5.mgh \
>--in lh.thickness.fsaverage.mgh \
>--sum segstats-ROI5.txt
> I encountered an error:
>
> ERROR: dimension inconsistency in source data
>
> Number of surface vertices = 126983
>
>Number of value vertices = 163842
>
>
> I tried as suggested in the forum the reshape-factor option as well as 
> the noreshape option for mri_vol2surf and mri_surf2surf. With no 
> success, I obtained a similar error.
>
> The ROI is extracted from another acquisition and is registered to the 
> T1. The T1 has been processed by following the classic pipeline using 
> recon-all … -all
>
> Any suggestions on how to fix that error or another pipeline that will 
> allow me to get the cortical thickness from inside my ROI?
>
> Thank you
>
>
> Elodie Boudes
> University of Calgary
>
>
>
>
>
>
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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] Results from R to Freesurfer

[Douglas N Greve]

On 03/08/2017 09:27 PM, Dorian P. wrote:
> Hi Freesurfers,
>
> I am using R to perform thickness analyses. All subjects are 
> transformed in fsaverage space and all values are placed in a matrix 
> with 327684 columns (163842 for each hemisphere). I put the results 
> back in a surface file (.asc format) and then convert it to a binary 
> Freesurfer format. I then open the files in Freesurfer to view them.
>
> Overall the results make sense and fall in the right places. But I am 
> concerned that some results fall into the corpus callosum, which, if I 
> remember correctly should not have any thickness value, and therefore 
> no results.
>
> Here is a screenshot:
> Inline image 1
>
> Can someone help my understand what might be wrong? Or, if this is 
> normal, why I am finding thickness results where there is no thickness?
Is this 5.3? The thickness may not be 0 in the medial wall, but non-zero 
values are meaningless and should be masked out or ignored.
>
> Is there a way to find label numbers for each vertex in fsaverage 
> space (i.e. list of parcel number for each vertex). This might be 
> useful to exclude certain vertices or compute summery statistics of 
> the results directly in R.
You can load the annotation into matlab with read_annotation.m
>
> Third question, is it possible to threshold the above map based on 
> minimal cluster area (i.e., in mri_surfcluster). If yes, do I need to 
> prepare a binary file with p-values for thresholding (0-1), or can I 
> use mri_surfcluster with t-score maps (0-Inf)?
You can use any map you want, you just have to specify the threshold 
correctly. Also, you will need to have a FWHM. To get this I would run 
an analysis in mri_glmfit using a design similar to what you used in R 
(small differences probably won't affect the FWHM measure).
>
> Thank you for your help.
> Dorian
>
>
>
> ___
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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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Re: [Freesurfer] Error mri_surf2surf FS6

[Douglas N Greve]

This was done to clear up a misunderstanding when using a target subject 
other than fsaverage. The way that 5.3 worked is that the data were 
actually sampled onto fsaverage through the ?h.sphere.reg. The target 
subject was only used in the smoothing process (if you even specified 
that as part of mris_preproc). This gave people the impression that they 
were sampling their data onto the target subject. To replicate 5.3, just 
specify fsaverage as the target and proceed as normal using your target 
after those commands. If you want to sample onto your target subject, 
then you will have to register each individual subject to the target, eg,

surfreg --s individualsubject --t average_AN_FS6_long_split

This will create ?h.average_AN_FS6_long_split.sphere.reg which can then 
be used in mris_preproc



On 03/09/2017 07:44 AM, Juergen Haenggi wrote:
> Dear FS experts
>
> we are trying to run statistics in FS6 Linux. Everthing worked fine 
> until we applied the command
> mris_preproc that called mri_surf2surf and produced the following error:
>
> #
>
> ---
> #@# 1/98 s1006_01.long.s1006_base Thu Mar  9 13:20:16 CET 2017 
> --
> ---
> mri_surf2surf --srcsubject s1006_01.long.s1006_base --srchemi rh 
> --srcsurfreg average_AN_FS6_long_split.sphere.reg --trgsubject 
> average_AN_FS6_long_split --trghemi rh --trgsurfreg sphere.reg --tval 
> ./average_AN_FS6_long_split/stats/lme_preproc/tmp.mris_preproc.3575/s1006_01.long.s1006_base.1.mgh
>  
> --sval 
> /usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.volume 
> --jac --sfmt curv --noreshape --cortex
> MRISread(/usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.average_AN_FS6_long_split.sphere.reg):
>  
> could not open file
> Source registration surface changed to 
> average_AN_FS6_long_split.sphere.reg
> Target registration surface changed to sphere.reg
>
> $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $
>
> setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
> cd /usr/local/freesurfer/subjects
> mri_surf2surf --srcsubject s1006_01.long.s1006_base --srchemi rh 
> --srcsurfreg average_AN_FS6_long_split.sphere.reg --trgsubject 
> average_AN_FS6_long_split --trghemi rh --trgsurfreg sphere.reg --tval 
> ./average_AN_FS6_long_split/stats/lme_preproc/tmp.mris_preproc.3575/s1006_01.long.s1006_base.1.mgh
>  
> --sval 
> /usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.volume 
> --jac --sfmt curv --noreshape --cortex
>
> sysname  Linux
> hostname psy-neuro-clt-Monster
> machine  x86_64
> user ego
> srcsubject = s1006_01.long.s1006_base
> srcval = 
> /usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.volume
> srctype= curv
> trgsubject = average_AN_FS6_long_split
> trgval = 
> ./average_AN_FS6_long_split/stats/lme_preproc/tmp.mris_preproc.3575/s1006_01.long.s1006_base.1.mgh
> trgtype=
> srcsurfreg = average_AN_FS6_long_split.sphere.reg
> trgsurfreg = sphere.reg
> srchemi= rh
> trghemi= rh
> frame  = 0
> fwhm-in= 0
> fwhm-out   = 0
> label-src  = rh.cortex.label
> label-trg  = rh.cortex.label
> OKToRevFaceOrder  = 1
> UseDualHemi = 0
> Reading source surface reg 
> /usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.average_AN_FS6_long_split.sphere.reg
> No such file or directory
> mri_surf2surf: could not read surface 
> /usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.average_AN_FS6_long_split.sphere.reg
> No such file or directory
>
> ###
>
> this line is odd:
>
> MRISread(/usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.average_AN_FS6_long_split.sphere.reg):
>  
> could not open file
>
> we are wondering why FS6 introduced the name of the target average 
> (average_AN_FS6_long_split) into the name of the individual subject 
> (rh.average_AN_FS6_long_split.sphere.reg) when looking 
> for s1006_01.long.s1006_base/surf/rh.sphere.reg.
>
> When using FS5.3.0 mris_preproc worked without this error.
>
> Any idea?
>
> Thanks in advance
> Best regards
> Jürgen
>
>
> -
> University of Zurich
> Dr. Jürgen Hänggi, Ph.D.
> Department of Psychology
> Division Neuropsychology
> Binzmuehlestrasse 14, PO Box 25
> 8050 Zurich, Switzerland
>
> 0041 44 635 73 97 (phone office)
> 0041 76 445 86 84 (phone mobile)
> 0041 44 635 74 09 (fax office)
> BIN 4.D.04 (office room number)
>
> j.haen...@psychologie.uzh.ch  (email)
> http://www.psychologie.uzh.ch/neuropsy/ (website)
> http://www.juergenhaenggi.ch (private website)
>
> This e-mail (and any attachment/s) contains confidential and/or privileged
> information. If you are not the intended recipient (or have received this
> e-mail in error) please notify the sender i

Re: [Freesurfer] mri_concat pet images into 1 template image

[Douglas N Greve]

If the 3 volumes are in register (ie, no motion between them), then I 
would just run the mri_concat command to create a single volume which is 
the average of the 3, then proceed as described.


On 03/09/2017 11:58 AM, Shane S wrote:
> Hi Doug,
>
> I want to derive a single averaged PET volume from the three 
> reconstructed 5 min acquisitions, expressed in detected counts. Then 
> we will divide the counts based on the cerebellum. Following that, I 
> want to use PetSurfer for partial volume correction and GLM 
> comparisons. May I upload the 3 images per subject?
>
> Thank you.
>
> -- 
> Shane S
>
> On 9 March 2017 at 16:18:33, Douglas N Greve 
> (gr...@nmr.mgh.harvard.edu ) wrote:
>
>> How are you planning on analyzing the different time points?
>>
>>
>> On 03/08/2017 05:33 PM, Shane S wrote:
>> > Dear Doug,
>> >
>> > My PET data is 3 x 5 minute acquisitions. Each subject has
>> > subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz and I am
>> > supposed to align and average them.
>> >
>> > Please advise.
>> >
>> > Thanks!
>> >
>> > --
>> > Shane Schofield
>> >
>> > On 8 March 2017 at 22:31:06, Douglas Greve (gr...@nmr.mgh.harvard.edu
>> > ) wrote:
>> >
>> >> No, the template is a within subject template used for registration.
>> >> If your pet data only has one frame (eg, FDG SUV), then you don't
>> >> need to run mri_convert or mri_concat, just use your pet image as the
>> >> template
>> >>
>> >>
>> >> On 3/8/17 11:11 AM, Shane S wrote:
>> >>> Hello Freesurfer,
>> >>>
>> >>> I have 3 PET images per individual. I am learning PetSurfer based on
>> >>> the Greve et al., 2014 paper.
>> >>>
>> >>> On the PetSurfer link, there are 2 methods.
>> >>>
>> >>> mri_convert pet.nii.gz —frame frameno template.nii.gz
>> >>> or
>> >>> mri_concat pet.nii.gz --mean —0 template.nii.gz
>> >>>
>> >>> What are the differences? My files are listed as
>> >>> subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz
>> >>>
>> >>> Is "mri_concat subject123_a.nii.gz, subject123_b.nii.gz,
>> >>> subject123_c.nii.gz —mean —o template.nii.gz” correct?
>> >>>
>> >>> Thank you for helping.
>> >>>
>> >>> Best Wishes,
>> >>>
>> >>> S
>> >>> --
>> >>> Shane Schofield
>> >>>
>> >>>
>> >>> ___
>> >>> Freesurfer mailing list
>> >>> Freesurfer@nmr.mgh.harvard.edu
>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >>
>> >> ___
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>> >>
>> >>
>> >> The information in this e-mail is intended only for the person to
>> >> whom it is
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>> >> the e-mail
>> >> contains patient information, please contact the Partners Compliance
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>> >
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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
>>
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>>
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>
>
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Re: [Freesurfer] mri_concat pet images into 1 template image

[Shane S]

Hi Doug,

I want to derive a single averaged PET volume from the three reconstructed 5 
min acquisitions, expressed in detected counts. Then we will divide the counts 
based on the cerebellum. Following that, I want to use PetSurfer for partial 
volume correction and GLM comparisons. May I upload the 3 images per subject?

Thank you.

-- 
Shane S

On 9 March 2017 at 16:18:33, Douglas N Greve (gr...@nmr.mgh.harvard.edu) wrote:

How are you planning on analyzing the different time points?  


On 03/08/2017 05:33 PM, Shane S wrote:  
> Dear Doug,  
>  
> My PET data is 3 x 5 minute acquisitions. Each subject has  
> subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz and I am  
> supposed to align and average them.  
>  
> Please advise.  
>  
> Thanks!  
>  
> --  
> Shane Schofield  
>  
> On 8 March 2017 at 22:31:06, Douglas Greve (gr...@nmr.mgh.harvard.edu  
> ) wrote:  
>  
>> No, the template is a within subject template used for registration.  
>> If your pet data only has one frame (eg, FDG SUV), then you don't  
>> need to run mri_convert or mri_concat, just use your pet image as the  
>> template  
>>  
>>  
>> On 3/8/17 11:11 AM, Shane S wrote:  
>>> Hello Freesurfer,  
>>>  
>>> I have 3 PET images per individual. I am learning PetSurfer based on  
>>> the Greve et al., 2014 paper.  
>>>  
>>> On the PetSurfer link, there are 2 methods.  
>>>  
>>> mri_convert pet.nii.gz —frame frameno template.nii.gz  
>>> or  
>>> mri_concat pet.nii.gz --mean —0 template.nii.gz  
>>>  
>>> What are the differences? My files are listed as  
>>> subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz  
>>>  
>>> Is "mri_concat subject123_a.nii.gz, subject123_b.nii.gz,  
>>> subject123_c.nii.gz —mean —o template.nii.gz” correct?  
>>>  
>>> Thank you for helping.  
>>>  
>>> Best Wishes,  
>>>  
>>> S  
>>> --  
>>> Shane Schofield  
>>>  
>>>  
>>> ___  
>>> Freesurfer mailing list  
>>> Freesurfer@nmr.mgh.harvard.edu  
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  
>>  
>> ___  
>> Freesurfer mailing list  
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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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--  
Douglas N. Greve, Ph.D.  
MGH-NMR Center  
gr...@nmr.mgh.harvard.edu  
Phone Number: 617-724-2358  
Fax: 617-726-7422  

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Re: [Freesurfer] glmfit error / group analysis

[Douglas N Greve]

The design matrix does not match the FSGD file. It could be because you 
have commas (i,e ",") instead of decimal points (ie, ".") in the FSGD 
file. Try replacing and rerunning.


On 03/08/2017 04:32 AM, teodora petrova wrote:
> Hello,
>
> I am trying to test for the effect of different variables on cortical 
> thickness. The variables (with type) are: index (continuous). 
> Gender(factor), Age(continuous),  Years of education (continuous),  
> Depression (factor),  Vascular comorbidity (factor), and MMSE 
> (continuous). Later, I need to correlate thickness with my variable of 
> interest (index). Depending on the results of the current analysis,  I 
> will choose which of the other variables will be my covariates.
>
> Here is what I attempted to do so far and the error I got:
>
> I have constructed the fsgd file according to the example with one 
> group and covariates (see attahced to this email). My contrasts look 
> like, for example: 0 1 0 0 0 0 0 (to test effects of gender), and 0 0 
> 1 0 0 0 0 (to test for the effects of age).
> I am following the commands in the Group Analysis tutorial. I pass 
> successfully mris_preproc and mri_surf2surf.
> When I get to mri_glmfit, I receive the error:
>
> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
>
> Possible problem with experimental design:
> Check for duplicate entries and/or lack of range of
> continuous variables within a class.
>
> 1. My command line is
> mri_glmfit --y lh.newindex.thickness.10.mgh --fsgd FSGD.fsgd dods  --C 
> index.mtx --C gender.mtx --C age.mtx --C education.mtx --C depression.mtx --C 
> vascularc.mtx --C MMSE.mtx --surf fsaverage lh --cortex  --glmdir 
> lh.newindex.glmdir
> 2. Please find attachced my fsgd file
> 3. Find attached the Design matrix
>
> What is the best way to construct the fsgd and contrasts?
> In the version I am sending, I have demeaned all continuous variables. 
> Is that something you will recommend to do? (I tried the group 
> analysis with a fsgd file containing the normal, non-demeaned values, 
> but got the same error).
>
> Thank you for the help!
>
> Best,
> Teodora
>
>
>
>
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] mri_vol2surf

[Douglas N Greve]

didn't I respond to this earlier this week? the images appear to be 
binarized regions of interest and not whole (or ever partial) brain. To 
run the registration, you will need an actual brain. If you created the 
ROI from a brain image, then use that image to create the reg, then run 
vol2surf using that reg with the ROI as input


On 03/07/2017 03:02 PM, Redwan Maatoug wrote:
> Hi experts,
>
> I try to convert my volumetric nifti file to surface files.
>
> My nifti volumetric file looks like : 1. screenshot
> I have first registered the volumetric file using bbregister with this 
> command line :
> *bbregister --s fsaverage --mov segment_7.nii --reg segment_7.dat --t1 
> --init-coreg*
>
> then I have used the following command line and the file looks like 
> screenshot 1 attached :
> *tkregister2 --mov segment_7.nii --reg register7.dat --surf*
>
> And after that, I have tried to convert my volumetric file to surface 
> file with this command line :
>
> *mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh --o 
> ./segment_7-lh.nii --float2int round*
>
> But with this command when I load the file with freeview it does not 
> work and with tkregister the file is empty.
>
> Or this one :
>
> *mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh --o 
> ./segment_7-lh.w --out_type paint --float2int tkregister*
>
> But with this command I have this warning :
> Warning: all vertex values are zero
>
> Could you please help me to convert my volumetric files because I am 
> probably doing someting wrong. All my files come from an Atlas and I 
> just need to convert them to surfaces files.
>
> Thank you for your help,
> Redwan
>
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] mri_concat pet images into 1 template image

[Shane S]

Thank you very much!!

-- 
Shane S

On 9 March 2017 at 17:01:28, Douglas N Greve (gr...@nmr.mgh.harvard.edu) wrote:

If the 3 volumes are in register (ie, no motion between them), then I  
would just run the mri_concat command to create a single volume which is  
the average of the 3, then proceed as described.  


On 03/09/2017 11:58 AM, Shane S wrote:  
> Hi Doug,  
>  
> I want to derive a single averaged PET volume from the three  
> reconstructed 5 min acquisitions, expressed in detected counts. Then  
> we will divide the counts based on the cerebellum. Following that, I  
> want to use PetSurfer for partial volume correction and GLM  
> comparisons. May I upload the 3 images per subject?  
>  
> Thank you.  
>  
> --  
> Shane S  
>  
> On 9 March 2017 at 16:18:33, Douglas N Greve  
> (gr...@nmr.mgh.harvard.edu ) wrote:  
>  
>> How are you planning on analyzing the different time points?  
>>  
>>  
>> On 03/08/2017 05:33 PM, Shane S wrote:  
>> > Dear Doug,  
>> >  
>> > My PET data is 3 x 5 minute acquisitions. Each subject has  
>> > subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz and I am  
>> > supposed to align and average them.  
>> >  
>> > Please advise.  
>> >  
>> > Thanks!  
>> >  
>> > --  
>> > Shane Schofield  
>> >  
>> > On 8 March 2017 at 22:31:06, Douglas Greve (gr...@nmr.mgh.harvard.edu  
>> > ) wrote:  
>> >  
>> >> No, the template is a within subject template used for registration.  
>> >> If your pet data only has one frame (eg, FDG SUV), then you don't  
>> >> need to run mri_convert or mri_concat, just use your pet image as the  
>> >> template  
>> >>  
>> >>  
>> >> On 3/8/17 11:11 AM, Shane S wrote:  
>> >>> Hello Freesurfer,  
>> >>>  
>> >>> I have 3 PET images per individual. I am learning PetSurfer based on  
>> >>> the Greve et al., 2014 paper.  
>> >>>  
>> >>> On the PetSurfer link, there are 2 methods.  
>> >>>  
>> >>> mri_convert pet.nii.gz —frame frameno template.nii.gz  
>> >>> or  
>> >>> mri_concat pet.nii.gz --mean —0 template.nii.gz  
>> >>>  
>> >>> What are the differences? My files are listed as  
>> >>> subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz  
>> >>>  
>> >>> Is "mri_concat subject123_a.nii.gz, subject123_b.nii.gz,  
>> >>> subject123_c.nii.gz —mean —o template.nii.gz” correct?  
>> >>>  
>> >>> Thank you for helping.  
>> >>>  
>> >>> Best Wishes,  
>> >>>  
>> >>> S  
>> >>> --  
>> >>> Shane Schofield  
>> >>>  
>> >>>  
>> >>> ___  
>> >>> 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  
>> >>  
>> >>  
>> >> The information in this e-mail is intended only for the person to  
>> >> whom it is  
>> >> addressed. If you believe this e-mail was sent to you in error and  
>> >> the e-mail  
>> >> contains patient information, please contact the Partners Compliance  
>> >> HelpLine at  
>> >> http://www.partners.org/complianceline . If the e-mail was sent to  
>> >> you in error  
>> >> but does not contain patient information, please contact the sender  
>> >> and properly  
>> >> dispose of the e-mail.  
>> >  
>> >  
>> > ___  
>> > Freesurfer mailing list  
>> > Freesurfer@nmr.mgh.harvard.edu  
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  
>>  
>> --  
>> 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  
>  
>  
> ___  
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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  
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[Freesurfer] Adjust bbregister affine to target raw T1

[Christopher Markiewicz]

Hi all,

Suppose you have a sub-pipeline:

$ recon-all -s $SUBJ -i $T1 -all
$ bbregister --s $SUBJ --mov $EPI --init-fsl --t2 --reg bbreg.dat --fslmat
fsl.mat

Now `bbreg.dat`/`fsl.mat` is registered to
`$SUBJECTS_DIR/$SUBJ/mri/T1.mgz`; what's the best way to register to $T1?

I've tried:

$ tkregister2 --no-edit --mov $EPI --reg bbreg.dat --targ $T1 --fslregout
adjusted.mat

And that's clearly wrong, but I'm kind of stuck on where to go from here.
Anybody see where I'm going wrong?

Thanks,
Chris
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Re: [Freesurfer] Adjust bbregister affine to target raw T1

[Douglas N Greve]

that should have worked. what was the bbregister final cost function? It 
could have been that fsl did not provide a good initial registration. If 
you have v6, you can leave off --init-fsl and it will use mri_coreg 
(which is more robust).


On 03/09/2017 03:24 PM, Christopher Markiewicz wrote:
> Hi all,
>
> Suppose you have a sub-pipeline:
>
> $ recon-all -s $SUBJ -i $T1 -all
> $ bbregister --s $SUBJ --mov $EPI --init-fsl --t2 --reg bbreg.dat 
> --fslmat fsl.mat
>
> Now `bbreg.dat`/`fsl.mat` is registered to 
> `$SUBJECTS_DIR/$SUBJ/mri/T1.mgz`; what's the best way to register to $T1?
>
> I've tried:
>
> $ tkregister2 --no-edit --mov $EPI --reg bbreg.dat --targ $T1 
> --fslregout adjusted.mat
>
> And that's clearly wrong, but I'm kind of stuck on where to go from 
> here. Anybody see where I'm going wrong?
>
> Thanks,
> Chris
>
>
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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

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Re: [Freesurfer] Adjust bbregister affine to target raw T1

[Christopher Markiewicz]

Hi Doug,

This is the final line with "cost" in it:

MinCost: 0.862331 7440.183178 7411.264107 -1.819400

We're switching from FLIRT BBR (two-pass) to bbregister when there's a
reconstructed subject available, so I'm using `--init-fsl` to try to
minimize the differences in the pipeline in the two cases, but I can try
`--init-coreg` if there's something wrong with the initialization.

Thanks,
Chris


On Thu, Mar 9, 2017 at 3:29 PM, Douglas N Greve 
wrote:

> that should have worked. what was the bbregister final cost function? It
> could have been that fsl did not provide a good initial registration. If
> you have v6, you can leave off --init-fsl and it will use mri_coreg
> (which is more robust).
>
>
> On 03/09/2017 03:24 PM, Christopher Markiewicz wrote:
> > Hi all,
> >
> > Suppose you have a sub-pipeline:
> >
> > $ recon-all -s $SUBJ -i $T1 -all
> > $ bbregister --s $SUBJ --mov $EPI --init-fsl --t2 --reg bbreg.dat
> > --fslmat fsl.mat
> >
> > Now `bbreg.dat`/`fsl.mat` is registered to
> > `$SUBJECTS_DIR/$SUBJ/mri/T1.mgz`; what's the best way to register to
> $T1?
> >
> > I've tried:
> >
> > $ tkregister2 --no-edit --mov $EPI --reg bbreg.dat --targ $T1
> > --fslregout adjusted.mat
> >
> > And that's clearly wrong, but I'm kind of stuck on where to go from
> > here. Anybody see where I'm going wrong?
> >
> > Thanks,
> > Chris
> >
> >
> > ___
> > 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.
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Re: [Freesurfer] Results from R to Freesurfer

[Dorian P.]

Thank you Bruce, Douglas.

Yes, I think thicknesses were obtained with v 5.3.0. There might be errors
as Bruce pointed out, I am going now through all maps to check them. This
makes me think of a question. Volumetric template registrations sometimes
go wrong. Does this happen also to surface registrations in FS sometimes ???

I am using other statistics, not glm, but thanks for suggesting it. Data
are imported and exported in R using some R functions I built myself,
nothing fancy, just using intermediate text files to get what I want and
put it back for visualization.

Thank you

On Thu, Mar 9, 2017 at 11:23 AM, Douglas N Greve 
wrote:

>
>
> On 03/08/2017 09:27 PM, Dorian P. wrote:
> > Hi Freesurfers,
> >
> > I am using R to perform thickness analyses. All subjects are
> > transformed in fsaverage space and all values are placed in a matrix
> > with 327684 columns (163842 for each hemisphere). I put the results
> > back in a surface file (.asc format) and then convert it to a binary
> > Freesurfer format. I then open the files in Freesurfer to view them.
> >
> > Overall the results make sense and fall in the right places. But I am
> > concerned that some results fall into the corpus callosum, which, if I
> > remember correctly should not have any thickness value, and therefore
> > no results.
> >
> > Here is a screenshot:
> > Inline image 1
> >
> > Can someone help my understand what might be wrong? Or, if this is
> > normal, why I am finding thickness results where there is no thickness?
> Is this 5.3? The thickness may not be 0 in the medial wall, but non-zero
> values are meaningless and should be masked out or ignored.
> >
> > Is there a way to find label numbers for each vertex in fsaverage
> > space (i.e. list of parcel number for each vertex). This might be
> > useful to exclude certain vertices or compute summery statistics of
> > the results directly in R.
> You can load the annotation into matlab with read_annotation.m
> >
> > Third question, is it possible to threshold the above map based on
> > minimal cluster area (i.e., in mri_surfcluster). If yes, do I need to
> > prepare a binary file with p-values for thresholding (0-1), or can I
> > use mri_surfcluster with t-score maps (0-Inf)?
> You can use any map you want, you just have to specify the threshold
> correctly. Also, you will need to have a FWHM. To get this I would run
> an analysis in mri_glmfit using a design similar to what you used in R
> (small differences probably won't affect the FWHM measure).
> >
> > Thank you for your help.
> > Dorian
> >
> >
> >
> > ___
> > 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.
>
>
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Re: [Freesurfer] Results from R to Freesurfer

[Bruce Fischl]

Hi Dorian

you can load the aparc.annot for each subject and use it to chek if the 
spherical registration worked ok. It's easy enough to write a script to 
load these for each subject, then write a tif file with a medial view, and 
zip through them all with nmovie

cheers
Bruce
On Thu, 9 Mar 2017, Dorian P. wrote:

> Thank you Bruce, Douglas.
> Yes, I think thicknesses were obtained with v 5.3.0. There might be errors
> as Bruce pointed out, I am going now through all maps to check them. This
> makes me think of a question. Volumetric template registrations sometimes go
> wrong. Does this happen also to surface registrations in FS sometimes ???
> 
> I am using other statistics, not glm, but thanks for suggesting it. Data are
> imported and exported in R using some R functions I built myself, nothing
> fancy, just using intermediate text files to get what I want and put it back
> for visualization.
> 
> Thank you
> 
> On Thu, Mar 9, 2017 at 11:23 AM, Douglas N Greve 
> wrote:
> 
>
>   On 03/08/2017 09:27 PM, Dorian P. wrote:
>   > Hi Freesurfers,
>   >
>   > I am using R to perform thickness analyses. All subjects are
>   > transformed in fsaverage space and all values are placed in a
>   matrix
>   > with 327684 columns (163842 for each hemisphere). I put the
>   results
>   > back in a surface file (.asc format) and then convert it to a
>   binary
>   > Freesurfer format. I then open the files in Freesurfer to view
>   them.
>   >
>   > Overall the results make sense and fall in the right places.
>   But I am
>   > concerned that some results fall into the corpus callosum,
>   which, if I
>   > remember correctly should not have any thickness value, and
>   therefore
>   > no results.
>   >
>   > Here is a screenshot:
>   > Inline image 1
>   >
>   > Can someone help my understand what might be wrong? Or, if
>   this is
>   > normal, why I am finding thickness results where there is no
>   thickness?
>   Is this 5.3? The thickness may not be 0 in the medial wall, but
>   non-zero
>   values are meaningless and should be masked out or ignored.
>   >
>   > Is there a way to find label numbers for each vertex in
>   fsaverage
>   > space (i.e. list of parcel number for each vertex). This might
>   be
>   > useful to exclude certain vertices or compute summery
>   statistics of
>   > the results directly in R.
>   You can load the annotation into matlab with read_annotation.m
>   >
>   > Third question, is it possible to threshold the above map
>   based on
>   > minimal cluster area (i.e., in mri_surfcluster). If yes, do I
>   need to
>   > prepare a binary file with p-values for thresholding (0-1), or
>   can I
>   > use mri_surfcluster with t-score maps (0-Inf)?
>   You can use any map you want, you just have to specify the
>   threshold
>   correctly. Also, you will need to have a FWHM. To get this I
>   would run
>   an analysis in mri_glmfit using a design similar to what you
>   used in R
>   (small differences probably won't affect the FWHM measure).
>   >
>   > Thank you for your help.
>   > Dorian
>   >
>   >
>   >
>   > ___
>   > 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.
> 
> 
> 
>
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Results from R to Freesurfer

[Dorian P.]

Thanks. I created a video to loop through all my 170+ subjects in template
space:

https://drive.google.com/open?id=0BxHeqEv37qqDeGFWVnpSVkVobkk

I see some cases that have dramatic problems. I will need to check those
more carefully and probably do an inspection of each one in individual
space. Beside those, do you think the variability of values going in and
out of the medial wall is normal for most of the subjects? You can point at
specific cases with the number of the subject on the overlay menu (left).
Thickness values start at 0.001

Thanks for your help so far.

Dorian

On Thu, Mar 9, 2017 at 4:29 PM, Bruce Fischl 
wrote:

> Hi Dorian
>
> you can load the aparc.annot for each subject and use it to chek if the
> spherical registration worked ok. It's easy enough to write a script to
> load these for each subject, then write a tif file with a medial view, and
> zip through them all with nmovie
>
> cheers
> Bruce
> On Thu, 9 Mar 2017, Dorian P. wrote:
>
> > Thank you Bruce, Douglas.
> > Yes, I think thicknesses were obtained with v 5.3.0. There might be
> errors
> > as Bruce pointed out, I am going now through all maps to check them. This
> > makes me think of a question. Volumetric template registrations
> sometimes go
> > wrong. Does this happen also to surface registrations in FS sometimes ???
> >
> > I am using other statistics, not glm, but thanks for suggesting it. Data
> are
> > imported and exported in R using some R functions I built myself, nothing
> > fancy, just using intermediate text files to get what I want and put it
> back
> > for visualization.
> >
> > Thank you
> >
> > On Thu, Mar 9, 2017 at 11:23 AM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu>
> > wrote:
> >
> >
> >   On 03/08/2017 09:27 PM, Dorian P. wrote:
> >   > Hi Freesurfers,
> >   >
> >   > I am using R to perform thickness analyses. All subjects are
> >   > transformed in fsaverage space and all values are placed in a
> >   matrix
> >   > with 327684 columns (163842 for each hemisphere). I put the
> >   results
> >   > back in a surface file (.asc format) and then convert it to a
> >   binary
> >   > Freesurfer format. I then open the files in Freesurfer to view
> >   them.
> >   >
> >   > Overall the results make sense and fall in the right places.
> >   But I am
> >   > concerned that some results fall into the corpus callosum,
> >   which, if I
> >   > remember correctly should not have any thickness value, and
> >   therefore
> >   > no results.
> >   >
> >   > Here is a screenshot:
> >   > Inline image 1
> >   >
> >   > Can someone help my understand what might be wrong? Or, if
> >   this is
> >   > normal, why I am finding thickness results where there is no
> >   thickness?
> >   Is this 5.3? The thickness may not be 0 in the medial wall, but
> >   non-zero
> >   values are meaningless and should be masked out or ignored.
> >   >
> >   > Is there a way to find label numbers for each vertex in
> >   fsaverage
> >   > space (i.e. list of parcel number for each vertex). This might
> >   be
> >   > useful to exclude certain vertices or compute summery
> >   statistics of
> >   > the results directly in R.
> >   You can load the annotation into matlab with read_annotation.m
> >   >
> >   > Third question, is it possible to threshold the above map
> >   based on
> >   > minimal cluster area (i.e., in mri_surfcluster). If yes, do I
> >   need to
> >   > prepare a binary file with p-values for thresholding (0-1), or
> >   can I
> >   > use mri_surfcluster with t-score maps (0-Inf)?
> >   You can use any map you want, you just have to specify the
> >   threshold
> >   correctly. Also, you will need to have a FWHM. To get this I
> >   would run
> >   an analysis in mri_glmfit using a design similar to what you
> >   used in R
> >   (small differences probably won't affect the FWHM measure).
> >   >
> >   > Thank you for your help.
> >   > Dorian
> >   >
> >   >
> >   >
> >   > ___
> >   > 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://ma

Re: [Freesurfer] Error viewing corrected results

[Antonin Skoch]

Dear Sahil,

 I would suggest at first to make check of your GLM PALM setup by comparing 
mri_glmfit and PALM output files (using the same design and contrast):

1. values of gamma.mgh should correspond to values of *cope.mgh

2. values of F.mgh should be (*dpv_tstat.mgh) ^2.

3. values of sig.mgh should be {roughly) values of -log10(*dpv_tstat_uncp.mgh) 
- I am currently not sure why I do not get exact correspondence here.

4. When you threshold the sig.mgh by some threshold in freeview (let it be x) 
and use the same corresponding cluster-forming z-score threshold -C  in PALM 
computed as 
qnorm(1-10^-x/2) (and use two-sided hypothesis by specifying -twotail), your 
*clustere_tstat.mgz should show the clusters with the same shape (regardless of 
their values, the clusters will be defined by non-zero value, other vertices 
would be zero) as the thresholded display of sig.mgh (computed by -two sided 
hypothesis).

If there is any inconsistence, then there is probably something wrong with your 
PALM setup.

Antonin


Dear Antonin, 
 
Could you please have a look at the attached screen shot. This map is with 
full number of permutations, without -approx tail -n 500 -nouncorrected 
 
Here, I noticed that its only *_dpv_tstat.mgz which looks correct and 
giving very high negative value, close to that big cluster, small positive 
values at red clusters and the value changes when I change the position of 
cursor. 
 
*_dpv_tstat_fwep shows value of 1 mostly but shows between 0.97 and 1 
close/at the red clusters and 1 elsewhere, even at the big blue negative 
cluster. 
 
Third, *_clustere_tstat_fwep and *_clustere_tstat shows 1 and 0 
respectively everywhere, even at the big blue negative cluster. 
 
If there is something fishy with the analysis, would you mind looking at 
the data and the detailed commands I am using to run the analysis? 
 
Thanks a lot, 
Sahil 
 
On Wed, Mar 8, 2017 at 11:54 PM, Antonin Skoch  wrote: 
 
> Dear Sahil, 
> 
> to assure that there is no other issue with your setup, I would  recommend to 
> obtain cluster-wise p-pvalue of that big cluster to see if  it is reasonable, 
> i.e. if it is somewhat close to the significance. 
> 
> Therefore, I would load *_clustere_tstat_fwep and click to the  area of big 
> cluster and see what the values of the vertices in that  region are. 
> 
> Or, I would increase --thmax in mri_surfcluster to see the  cluster-wise 
> p-value(s). If you use --thmax 0. (or maybe 1), you  should see 
> cluster-wise FWER corrected p-values of all clusters formed  by used 
> cluster-forming threshold. 
> 
> I would also maybe try to switch-off tail approximation and run  it in full 
> number of permutations (i.e. do not use -approx tail -n 500  -nouncorrected). 
> 
> If there is no other issue, then yes, the conclusion would be,  that for the 
> used cluster-extent inference and currently set  cluster-forming threshold, 
> none of the clusters survived FWER correction  at cluster-wise p-value 
> threshold of 0.05. 
> 
> Antonin 
> 
> 
> 
> Dear Antonin, 
> 
> Setting minimum to 1.3 for *_clustere_tstat_fwep doesn't show any 
> significant cluster and similarly thresholded map *dpv_tstat.mgz also 
> doesn't show anything at -log10(0.05) = 1.3. As you said, it seems like 
> even though there is big cluster but after FWER correction, the 
> significance goes away. Actually, even when I removed -logp, I still do not 
> see any significant cluster. 
> 
> Next, I tried to use mri_surfcluster using following three commands 
> following instructions from the link you sent: 
> 
> mri_binarize --i Results_Left_clustere_tstat_fwep.mgz --min 1 --o p_bin.mgz 
> 
> mris_calc --output pmap_filter.mgz Results_Left_clustere_tstat_fwep.mgz sub 
> p_bin.mgz 
> 
> mri_surfcluster --in pmap_filter.mgz --subject fsaverage --hemi lh --surf 
> white --annot aparc.a2009s --thmin 0.0001 --thmax 0.05 --mask 
> glmdir/mask.mgh --sum summary --nofixmni 
> 
> This gives me 'zero' cluster in the summary file. 
> 
> If the above steps are correct, would you conclude that the LGI results are 
> not significant and un-reportable for publication purpose and I should give 
> a try to thickness, volume and area maps? 
> 
> Thanks you so much Antonin for all your help. 
> Sahil 
> 
> 
> 
> On Wed, Mar 8, 2017 at 3:05 PM, Antonin Skoch  wrote: 
> 
> > Dear Sahil, 
> > 
> > If you used -logp as Anderson suggested, you should set your min to 1.3 to 
> > threshold your *_clustere_tstat_fwep map and see the clusters. 
> > 
> > What is the value of *_clustere_tstat_fwep in the region of the big 
> > cluster seen at thresholded map *dpv_tstat.mgz ?  This should correspond to 
> > your -log10(p) of your cluster. 
> > 
> > I personally did not use -logp and use the mri_surfcluster for the 
> > reporting of the clusters, as I wrote in previous mail here: 
> > 
> > freesurfer@nmr.mgh.harvard.edu/msg52042.html" 
> > title="http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52042.html";
> >  
> > targe

Re: [Freesurfer] Results from R to Freesurfer

[Bruce Fischl]

you could create a mask that is the AND of all your subject masks I suppose


On Thu, 9 Mar 2017, Dorian P. wrote:


Thanks. I created a video to loop through all my 170+ subjects in template
space:
https://drive.google.com/open?id=0BxHeqEv37qqDeGFWVnpSVkVobkk

I see some cases that have dramatic problems. I will need to check those
more carefully and probably do an inspection of each one in individual
space. Beside those, do you think the variability of values going in and out
of the medial wall is normal for most of the subjects? You can point at
specific cases with the number of the subject on the overlay menu (left).
Thickness values start at 0.001

Thanks for your help so far.

Dorian

On Thu, Mar 9, 2017 at 4:29 PM, Bruce Fischl 
wrote:
  Hi Dorian

  you can load the aparc.annot for each subject and use it to chek
  if the
  spherical registration worked ok. It's easy enough to write a
  script to
  load these for each subject, then write a tif file with a medial
  view, and
  zip through them all with nmovie

  cheers
  Bruce
  On Thu, 9 Mar 2017, Dorian P. wrote:

  > Thank you Bruce, Douglas.
  > Yes, I think thicknesses were obtained with v 5.3.0. There
  might be errors
  > as Bruce pointed out, I am going now through all maps to check
  them. This
  > makes me think of a question. Volumetric template
  registrations sometimes go
  > wrong. Does this happen also to surface registrations in FS
  sometimes ???
  >
  > I am using other statistics, not glm, but thanks for
  suggesting it. Data are
  > imported and exported in R using some R functions I built
  myself, nothing
  > fancy, just using intermediate text files to get what I want
  and put it back
  > for visualization.
  >
  > Thank you
  >
  > On Thu, Mar 9, 2017 at 11:23 AM, Douglas N Greve
  
  > wrote:
  >
  >
  >       On 03/08/2017 09:27 PM, Dorian P. wrote:
  >       > Hi Freesurfers,
  >       >
  >       > I am using R to perform thickness analyses. All
  subjects are
  >       > transformed in fsaverage space and all values are
  placed in a
  >       matrix
  >       > with 327684 columns (163842 for each hemisphere). I
  put the
  >       results
  >       > back in a surface file (.asc format) and then convert
  it to a
  >       binary
  >       > Freesurfer format. I then open the files in Freesurfer
  to view
  >       them.
  >       >
  >       > Overall the results make sense and fall in the right
  places.
  >       But I am
  >       > concerned that some results fall into the corpus
  callosum,
  >       which, if I
  >       > remember correctly should not have any thickness
  value, and
  >       therefore
  >       > no results.
  >       >
  >       > Here is a screenshot:
  >       > Inline image 1
  >       >
  >       > Can someone help my understand what might be wrong?
  Or, if
  >       this is
  >       > normal, why I am finding thickness results where there
  is no
  >       thickness?
  >       Is this 5.3? The thickness may not be 0 in the medial
  wall, but
  >       non-zero
  >       values are meaningless and should be masked out or
  ignored.
  >       >
  >       > Is there a way to find label numbers for each vertex
  in
  >       fsaverage
  >       > space (i.e. list of parcel number for each vertex).
  This might
  >       be
  >       > useful to exclude certain vertices or compute summery
  >       statistics of
  >       > the results directly in R.
  >       You can load the annotation into matlab with
  read_annotation.m
  >       >
  >       > Third question, is it possible to threshold the above
  map
  >       based on
  >       > minimal cluster area (i.e., in mri_surfcluster). If
  yes, do I
  >       need to
  >       > prepare a binary file with p-values for thresholding
  (0-1), or
  >       can I
  >       > use mri_surfcluster with t-score maps (0-Inf)?
  >       You can use any map you want, you just have to specify
  the
  >       threshold
  >       correctly. Also, you will need to have a FWHM. To get
  this I
  >       would run
  >       an analysis in mri_glmfit using a design similar to what
  you
  >       used in R
  >       (small differences probably won't affect the FWHM
  measure).
  >       >
  >       > Thank you for your help.
  >       > Dorian
  >       >
  >       >
  >       >
  >       > ___
  >       > Freesurfer mailing list
  >       > Freesurfer@nmr.mgh.harvard.edu
  >       >
  https://mail.nmr.mgh.harvard.edu/mailman/l

[Freesurfer] subject directory

[Limachia, Gaurang (NIH/NINDS) [F]]

Dear Freesurfer Experts,

I want to customize the directory so I can run the following command

mris_preproc --fsgd gender_age.fsgd   --cache-in thickness.fwhm10.fsaverage   
--target fsaverage   --hemi lh   --out lh.gender_age.thickness.10.mgh

However, after running this command it keeps checking in the wrong directory 
for the files. How do I change the directory, do I change it in the FSGD file I 
made or somewhere else? I ran the recon-all qcache, but I need to run this on 
the previously cached data. I would greatly appreciate it if you can assist me 
with this problem.

Best Regards,

Gaurang Shyam LImachia
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[Freesurfer] Inflation of RH only

[XJ Kang]

Hi Experts,

I am trying to inflate the brains with lesions in the LHs. The inflation 
failed because of those lesions. I need the RH data from the files 
"mri/wmparc.mgz" and "stats/rh.aparc.stats". Here are what I did:


1. Use "recon-all -hemi rh" to inflate the RH only but the inflation 
stopped at the step "mris_volmask". it needs the "lh.white" file. Then I 
tried to run the following steps manually, but not succeed.


2. Replace the LH by RH to construct a new brain image (RH+RH) for 
inflation. Yes the inflation finished. I can find the RH data. However, 
I'd like to verify the RH data from the inflation of "RH+RH" are the 
same as those from "LH+RH" by comparing the two inflations of a healthy 
brain. What I found is that the parcellations of the same RH are little 
different with different LH structures, especially curvature and 
thickness. I'd like to know if this is true. In other words, are the 
inflations of LH and RH are correlated?


Any more suggestions to get the RH parcellation data for brains with 
lesions in LH? Thank you for your time.


XJ Kang



On 7/7/2016 11:11 AM, Bruce Fischl wrote:

Hi XJ

this is a known problem but we haven't gotten to fixing it yet. Do you 
need it to complete that step? It is pretty close to the end so it may 
be that the error doesn't effect you

cheers
Bruce

On Thu, 7 Jul 2016, Kang, XJ wrote:


Hi,

I am trying to inflate right hemisphere only using the commands:

recon-all -autorecon2 -hemi rh  -subjid 160526
recon-all -autorecon3 -hemi rh  -subjid 160526

The inflation stopped at the step:
mris_volmask --label_left_white 2 --label_left_ribbon 3 
--label_right_white

41 --label_right_ribbon 42 --save_ribbon 160526

SUBJECTS_DIR is /home/sata3/FreeSurfer/Subjects
MRISread(/home/sata3/FreeSurfer/Subjects/160526/surf/lh.white): could 
not

open file

The program "mris_volmask" needs to read "lh.white", which is not 
generated.
Any expert has any suggestions? Maybe I didn't use the commands 
correctly?


Thank you for your help.

XJ Kang





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[Freesurfer] WM/pial edits

[Octavian Lie]

Dear All,

A simple issue of precedence. In the recon-all pipeline, wm edits take
precedence to pial edits.
If there are both wm and pial defects, should one apply edits sequentially,
say on brainmask.mgz (first wm edits, rerun recon-all say recon-all
-autorecon2 -wm, then do pial edits, rerun recon-all say recon-all
-autorecon2 -pial) or to some extent pial edits influence the final surface
generation in conjunction to wm edits (understood that the latter may
influence more the final form than the former -pial- edits), in that case
one may do both edits, then run -autorecon2 -wm only.

Please advise,
Octavian
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Re: [Freesurfer] subject directory

[Douglas Greve]

can you send the terminal entire output that includes the error?


On 3/9/17 7:57 PM, Limachia, Gaurang (NIH/NINDS) [F] wrote:


Dear Freesurfer Experts,

I want to customize the directory so I can run the following command

mris_preproc --fsgd gender_age.fsgd   --cache-in 
thickness.fwhm10.fsaverage   --target fsaverage   --hemi lh   --out 
lh.gender_age.thickness.10.mgh


However, after running this command it keeps checking in the wrong 
directory for the files. How do I change the directory, do I change it 
in the FSGD file I made or somewhere else? I ran the recon-all qcache, 
but I need to run this on the previously cached data. I would greatly 
appreciate it if you can assist me with this problem.


Best Regards,

Gaurang Shyam LImachia



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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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