Re: [Freesurfer] Cortical surface

[郑凤莲]

External Email - Use Caution

OK. Thank you very much.


Sincerely,
Zheng






At 2018-08-13 01:15:26, "Douglas Greve"  wrote:
You can break up the aparc annotation into labels (mri_annotation2label), then 
create a new annotation with just the insula (mris_label2annot)



On 8/12/18 5:17 AM, 郑凤莲 wrote:


External Email - Use Caution

Dear experts,
  I an using FS 6.0 for cortical reconstructions.  I can show whole brain 
regions (tksurfer...), as shown in the picture. However,  I just want to show 
insular region. Is there any way to complete it? I am looking forward to your 
reply. Thanks very much.
Sincerely,
Zheng




 




___
Freesurfer mailing list
freesur...@nmr.mgh.harvard.eduhttps://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.

Re: [Freesurfer] Stats2table_bash.sh script

[Schumman Resonance]

External Email - Use Caution

Thanks Robert, I guess my main issue is that I don't fully understand how
the script works:


[1] export SUBJECTS_DIR=*$PWD*
*[2] list="`ls -d */`"*
[3] asegstats2table --subjects *$list *--meas volume --skip --statsfile
wmparc.stats --all-segs --tablefile wmparc_stats.txt

I was assuming the variable $list would give SUBJECTS to --subjects based
on each directory where .stats files are.
I don't fully understand how lines [1] and [2] work.

Apologies if I'm not conveying my struggle with proper coding language :)



On Sun, Aug 12, 2018 at 2:03 PM, Dicamillo, Robert <
rdicami...@mgh.harvard.edu> wrote:

> Hello K,
>
> If you type
>
> $ asegstats2table --help
>
> you will see that you can specify subjects on the command line as, e.g.,
> for bert as
>
> —subjects bert
> or apparently
> -s bert
>
> It looks like the subjects option expects the name for at least one
> subjects (data),
> but the help output says you can list more than one subjects name as the
> argument to
> —subjects
>
> On Aug 12, 2018, at 12:31 PM, Schumman Resonance 
> wrote:
>
> External Email - Use Caution
>
>
> Hi,
>
> I'm trying to run the Stats2table_bash.sh script from Jamaan Alghamdi &
> Dr. Vanessa Sluming.
>
> And I get This error:
>
>   File "/Applications/freesurfer/bin/asegstats2table", line 195
> print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
>   ^
> SyntaxError: invalid syntax
>   File "/Applications/freesurfer/bin/asegstats2table", line 195
> print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
>   ^
> SyntaxError: invalid syntax
>   File "/Applications/freesurfer/bin/aparcstats2table", line 156
> print 'ERROR: atleast 1 subject must be provided'
> .
> .
> .
>
>
>
> This is my set up:
>
>
> _
>
>
>  freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /Applications/freesurfer
> FSFAST_HOME   /Applications/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /Users/schumman/data
> MNI_DIR   /Applications/freesurfer/mni
> FSL_DIR   /usr/local/fsl
>
> _
>
>
> This is the line from SetUpFreeSurfer.sh for my subjects directory
> 
>
> # Set this to your subjects/ dir, usually freesurfer/subjects/
> if [ -z $SUBJECTS_DIR ]; then
> export SUBJECTS_DIR=/Users/schumman/data
>
>
> __
>
> And I modified in their script to my FREESURFER_HOME as below
>
>
> #!/bin/bash
> path=`dirname $0`
> sleep 1
> cd $path
> echo "This bash script will create table from ?.stats files"
> echo "Written by Jamaan Alghamdi & Dr. Vanessa Sluming"
> echo "University of Liverpool"
> echo "jamaan.algha...@gmail.com"
> echo "http://www.easyneuroimaging.com;
> echo "20/12/2010
>
> "
>
>
> export FREESURFER_HOME=/Applications/freesurfer
> sleep 1
> source $FREESURFER_HOME/SetUpFreeSurfer.sh
> sleep 1
>
> export SUBJECTS_DIR=$PWD
> list="`ls -d */`"
> asegstats2table --subjects $list --meas volume --skip --statsfile
> wmparc.stats --all-segs --tablefile wmparc_stats.txt
> .
> .
> .
>
>
> I run the script from my_subject_directory.
>
> I suspect this is something very obvious I'm not able to see and I
> apologize for such a basic question, any help would be much appreciated.
>
> Thanks,
> K
>
>
>
> ___
> 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


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 

Re: [Freesurfer] fsaverage6 ?h.cortex.flat.patch files

[Bruce Fischl]

oh, maybe we never got around to writing a write_patch.m. We'll put one 
together and send it to you

Bruce
On Sun, 12 Aug 2018, Dinicola, Lauren wrote:


Hi Dr. Fischl,
Thank you so much for this response. This is a great idea, but I have not yet 
been successful with
writing out the adjusted structure to a ?h.cortex.flat.patch file. 
Is there a specific command for writing a patch?

Thank you again,

Lauren

On Wed, Aug 8, 2018 at 3:04 PM, Bruce Fischl  wrote:
  sorry, no. You could create them fairly easily from fsaverage7, since the
  fsaverage6 is a subset of the vertices in 7. Just pick out the locations 
of
  the fsaverage6 vertices from the fsaverage7 flat map and write it out as a
  flat map (easy to do in matlab for example)

  On Wed,
  8 Aug 2018, Dinicola, Lauren wrote:

  > Hi all,
  > We are hoping to visualize flat maps of surface data sampled to 
fsaverage6. Do
  'flat.patch' files
  > exist already for fsaverage6?
  >
  > Thank you for any help,
  >
  > Lauren DiNicola
  >
  >
___
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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Stats2table_bash.sh script

[Dicamillo, Robert]

Hello K,

If you type

$ asegstats2table --help

you will see that you can specify subjects on the command line as, e.g., for 
bert as

—subjects bert
or apparently
-s bert

It looks like the subjects option expects the name for at least one subjects 
(data),
but the help output says you can list more than one subjects name as the 
argument to
—subjects

On Aug 12, 2018, at 12:31 PM, Schumman Resonance 
mailto:schumm...@gmail.com>> wrote:


External Email - Use Caution


Hi,

I'm trying to run the Stats2table_bash.sh script from Jamaan Alghamdi & Dr. 
Vanessa Sluming.

And I get This error:

  File "/Applications/freesurfer/bin/asegstats2table", line 195
print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
  ^
SyntaxError: invalid syntax
  File "/Applications/freesurfer/bin/asegstats2table", line 195
print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
  ^
SyntaxError: invalid syntax
  File "/Applications/freesurfer/bin/aparcstats2table", line 156
print 'ERROR: atleast 1 subject must be provided'
.
.
.



This is my set up:


_


 freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer
FSFAST_HOME   /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Users/schumman/data
MNI_DIR   /Applications/freesurfer/mni
FSL_DIR   /usr/local/fsl

_


This is the line from SetUpFreeSurfer.sh for my subjects directory


# Set this to your subjects/ dir, usually freesurfer/subjects/
if [ -z $SUBJECTS_DIR ]; then
export SUBJECTS_DIR=/Users/schumman/data


__

And I modified in their script to my FREESURFER_HOME as below


#!/bin/bash
path=`dirname $0`
sleep 1
cd $path
echo "This bash script will create table from ?.stats files"
echo "Written by Jamaan Alghamdi & Dr. Vanessa Sluming"
echo "University of Liverpool"
echo "jamaan.algha...@gmail.com"
echo "http://www.easyneuroimaging.com"
echo "20/12/2010

"


export FREESURFER_HOME=/Applications/freesurfer
sleep 1
source $FREESURFER_HOME/SetUpFreeSurfer.sh
sleep 1

export SUBJECTS_DIR=$PWD
list="`ls -d */`"
asegstats2table --subjects $list --meas volume --skip --statsfile wmparc.stats 
--all-segs --tablefile wmparc_stats.txt
.
.
.


I run the script from my_subject_directory.

I suspect this is something very obvious I'm not able to see and I apologize 
for such a basic question, any help would be much appreciated.

Thanks,
K



___
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.

Re: [Freesurfer] fsaverage6 ?h.cortex.flat.patch files

[Dinicola, Lauren]

Hi Dr. Fischl,

Thank you so much for this response. This is a great idea, but I have not
yet been successful with writing out the adjusted structure to a
?h.cortex.flat.patch file.
Is there a specific command for writing a patch?

Thank you again,

Lauren

On Wed, Aug 8, 2018 at 3:04 PM, Bruce Fischl 
wrote:

> sorry, no. You could create them fairly easily from fsaverage7, since the
> fsaverage6 is a subset of the vertices in 7. Just pick out the locations
> of
> the fsaverage6 vertices from the fsaverage7 flat map and write it out as a
> flat map (easy to do in matlab for example)
>
> On Wed,
> 8 Aug 2018, Dinicola, Lauren wrote:
>
> > Hi all,
> > We are hoping to visualize flat maps of surface data sampled to
> fsaverage6. Do 'flat.patch' files
> > exist already for fsaverage6?
> >
> > Thank you for any help,
> >
> > Lauren DiNicola
> >
> >
> ___
> 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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Stats2table_bash.sh script

[Dicamillo, Robert]

Hello K,

If you type

$ asegstats2table --help

you will see that you can specify subjects on the command line as, e.g., for 
bert as

—subjects bert
or apparently
-s bert

It looks like the subjects option expects the name for at least one subjects 
(data),
but the help output says you can list more than one subjects name as the 
argument to
—subjects

On Aug 12, 2018, at 12:31 PM, Schumman Resonance 
mailto:schumm...@gmail.com>> wrote:


External Email - Use Caution


Hi,

I'm trying to run the Stats2table_bash.sh script from Jamaan Alghamdi & Dr. 
Vanessa Sluming.

And I get This error:

  File "/Applications/freesurfer/bin/asegstats2table", line 195
print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
  ^
SyntaxError: invalid syntax
  File "/Applications/freesurfer/bin/asegstats2table", line 195
print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
  ^
SyntaxError: invalid syntax
  File "/Applications/freesurfer/bin/aparcstats2table", line 156
print 'ERROR: atleast 1 subject must be provided'
.
.
.



This is my set up:


_


 freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer
FSFAST_HOME   /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Users/schumman/data
MNI_DIR   /Applications/freesurfer/mni
FSL_DIR   /usr/local/fsl

_


This is the line from SetUpFreeSurfer.sh for my subjects directory


# Set this to your subjects/ dir, usually freesurfer/subjects/
if [ -z $SUBJECTS_DIR ]; then
export SUBJECTS_DIR=/Users/schumman/data


__

And I modified in their script to my FREESURFER_HOME as below


#!/bin/bash
path=`dirname $0`
sleep 1
cd $path
echo "This bash script will create table from ?.stats files"
echo "Written by Jamaan Alghamdi & Dr. Vanessa Sluming"
echo "University of Liverpool"
echo "jamaan.algha...@gmail.com"
echo "http://www.easyneuroimaging.com"
echo "20/12/2010

"


export FREESURFER_HOME=/Applications/freesurfer
sleep 1
source $FREESURFER_HOME/SetUpFreeSurfer.sh
sleep 1

export SUBJECTS_DIR=$PWD
list="`ls -d */`"
asegstats2table --subjects $list --meas volume --skip --statsfile wmparc.stats 
--all-segs --tablefile wmparc_stats.txt
.
.
.


I run the script from my_subject_directory.

I suspect this is something very obvious I'm not able to see and I apologize 
for such a basic question, any help would be much appreciated.

Thanks,
K



___
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.

Re: [Freesurfer] T1 mapping

[Douglas Greve]

On 8/10/18 3:26 PM, Fotiadis, Panagiotis wrote:


Hi Doug,


Thanks for your response! I had a couple follow-up questions:


1) If I used mri_fit_parms to calculate the T1 maps, then created a 
surface mid-cortex (with mris_expand) with that T1 map as a reference, 
and uploaded that file into MATLAB through MRIread, would the 
resulting values represent absolute "pure" T1 values?



If by "pure" you mean quantitative (ie, values in milisec), then yes.



2) Even though we are scanning on a Siemens scanner we have been 
acquiring a tfl_mgh_multiecho_4E_P2_1MM_ISO sequence. Do you think I 
could do T1 mapping based on that sequence (with the same method as 
the one described in the previous question)?


Multiecho does not help for measuring T1. But if you have multiple flip 
angles or multiple inversions with you rmultiecho, then you can use the 
multiecho data to compute T1



Thanks again, and I apologize for the potential triviality of the 
questions!



Best,

Panos


Panagiotis Fotiadis
Senior Imaging Research Technologist
J. P. Kistler Stroke Research Center, Department of Neurology
Massachusetts General Hospital, Boston, MA
T: (617) 643-3869

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas Greve 


*Sent:* Friday, August 10, 2018 1:59:47 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] T1 mapping
mri_fit_parms should do it. BTW, if you are using a siemens scanner, 
you should just collect an MP2RAGE. That automatically outputs a 
quantitative T1 map using the two inversion technique. The results are 
much more accurate than using multiple flip angles


On 8/8/18 5:00 PM, Fotiadis, Panagiotis wrote:


Hello,


I am interested in doing some T1-mapping analyses on some ex vivo 
brains. We have collected flash sequences under multiple flip angles 
(5, 10, 15, 20, 25 and 30). How would you suggest that I proceed? 
Should I use the mri_ms_fitparms to come up with the T1 maps for each 
subject and then maybe calculate the signal intensity 1mm into the 
cortex, or is there another way that you would recommend?



Thanks in advance for any advice!


Best,

Panos


Panagiotis Fotiadis
Senior Imaging Research Technologist
J. P. Kistler Stroke Research Center, Department of Neurology
Massachusetts General Hospital, Boston, MA
T: (617) 643-3869


___
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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Plotting QDEC results

[Douglas Greve]

On 8/11/18 12:02 PM, Avi Gharehgazlou wrote:


External Email - Use Caution

Thank you for your reply. I chose the 1.3 threshold based on LGI 
papers in the ASD literature, but I will use 2.0.

2 is still too low. You'd need at least 3.


1. By permutation do you mean FDR correction?

no, permutation and FDR are different


2. If I use monte carlo at 2.0 (0.01 p-value) would this be okay for 
LGI, or do you still recommend FDR correction?
No, 2 is too low. At least 3, and that may be too low. Permutation will 
be better.


Many thanks,

Avi


On Fri, Aug 10, 2018 at 1:53 PM, Douglas Greve > wrote:


Each row is a subject and each column is a cluster. BTW, a
threshold of 1.3 is way too low for lGI. If you want to use a
threshold that low, you should use permutation instead of monte
carlo (in general, permutation is better, but certainly for lGI).

On 8/9/18 1:39 PM, Avi Gharehgazlou wrote:


External Email - Use Caution

Hi experts,

I looked at association between LGI and a behavioural scale on
QDEC. after the analysis, to plot the significant clusters/
blobs, I wanted to export LGI values for each subject from each
significant blob and based on instructions in previous archives I
ran the following command line:

mri_glmfit-sim –glmdir (qdec output directory) --cache 1.3 abs

which generated a "cache.th13.abs.y.ocn.dat" file. This file
contains 3 columns and 36 rows. I'm assuming the values in the
three columns correspond to LGI values for each significant blob
for each subject? (I had 3 significant blobs and 36 participants)

Will you please confirm I am doing (and interpreting) this correctly?

Thanks so much,

Avi


___
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


___
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.

Re: [Freesurfer] coregistering with bbregister

[Douglas Greve]

On 8/10/18 6:48 PM, Ben M wrote:


External Email - Use Caution

Hi Doug,

Thank you for your suggestions, I'll try them.
Could you please let me know if my code is actually doing what I 
intend it to do? Specifically, the idea is to perform 
functional-to-structural registration.


so first I did
$ bbregister --t2 --reg /data/bbregister/reg.dat --mov 
/data/mean_func.nii.gz --s 001
That is right. The only thing I would change is to use reg.lta instead 
of reg.dat. The lta file has more info in it and we're trying to get 
people to move to it.


I'm not sure if the --mov image should be the motion-corrected mean 
functional image or the skull-stripped anatomical image. I think if I 
want to do functional-to-structural registration it should actually be 
the anatomical image as --mov right? Or it doesn't matter which one I 
choose?

Yes, it matters. The mov should be the functional.


I then did
$ mri_vol2vol --mov /data/bet_structural.nii.gz --targ 
/data/brain.nii.gz --o /data/coregistered_structural.nii.gz --reg  
/data/bbregister/reg.dat --inv –-nearest
 which I thinks applies the transformation matrix to the structural 
image, am I correct? In this case it would be a 
structural-to-functional registration I think.

Did you see the examples (run mri_vol2vol --help)
So, if I intend to perform functional-to-structural registration I 
should actually rather do


$ bbregister --t2 --reg /data/bbregister/reg.dat --mov 
/data/bet_structural.nii.gz --s 001
$ mri_vol2vol --mov /data/mean_func.nii.gz --targ /data/brain.nii.gz 
--o /data/coregistered_functional.nii.gz --reg  
/data/bbregister/reg.dat --inv –-nearest


Could you please confirm if this is correct?

Thank you very much,
Ben




Sometimes the FSL initialization will fail. If you are using FS version
6, then run it without specifying --init-fsl and it will use mri_coreg,
which is more robust. If your anatomical and functional were acquired at
the same time, you might be able to get away with --init-header instead.

On 8/9/18 2:12 PM, Ben M wrote:
>//>/External Email - Use Caution />//>/Hi, />/I'm trying to coregister the strucural image to the mean functional />/image using bbregister, so after reconall I did: />//>/bbregister --t2 --init-fsl --reg /data/bbregister/reg.dat --mov />//data/mean_func.nii.gz --s 001 />//>/bet /data/structural.nii.gz /data/bet_structural.nii.gz />//>/#brain.nii.gz is the brain.mgz from reconall output (in freesurfer 
space) />/mri_vol2vol --mov /data/bet_structural.nii.gz --targ />//data/brain.nii.gz --o /data/coregistered_structural.nii.gz --reg />//data/bbregister/reg.dat --inv –-nearest />//>/But when I load the coregistered_structural.nii.gz and the />/mean_func.nii.gz they are not aligned. I'm sure I'm doing something />/wrong, could someone help me figure it out please? />//>/Thanks in advance, />/Ben/




___
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.

Re: [Freesurfer] Cortical surface

[Douglas Greve]

You can break up the aparc annotation into labels 
(mri_annotation2label), then create a new annotation with just the 
insula (mris_label2annot)



On 8/12/18 5:17 AM, 郑凤莲 wrote:


External Email - Use Caution

Dear experts,
  I an using FS 6.0 for cortical reconstructions.  I can show whole 
brain regions (tksurfer...), as shown in the picture. However,  I just 
want to show insular region. Is there any way to complete it? I am 
looking forward to your reply. Thanks very much.

Sincerely,
Zheng




___
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] Stats2table_bash.sh script

[Schumman Resonance]

External Email - Use Caution

Hi,

I'm trying to run the Stats2table_bash.sh script from Jamaan Alghamdi & Dr.
Vanessa Sluming.

And I get This error:

  File "/Applications/freesurfer/bin/asegstats2table", line 195
print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
  ^
SyntaxError: invalid syntax
  File "/Applications/freesurfer/bin/asegstats2table", line 195
print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
  ^
SyntaxError: invalid syntax
  File "/Applications/freesurfer/bin/aparcstats2table", line 156
print 'ERROR: atleast 1 subject must be provided'
.
.
.



This is my set up:


_


 freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer
FSFAST_HOME   /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Users/schumman/data
MNI_DIR   /Applications/freesurfer/mni
FSL_DIR   /usr/local/fsl

_


This is the line from SetUpFreeSurfer.sh for my subjects directory


# Set this to your subjects/ dir, usually freesurfer/subjects/
if [ -z $SUBJECTS_DIR ]; then
export SUBJECTS_DIR=/Users/schumman/data


__

And I modified in their script to my FREESURFER_HOME as below


#!/bin/bash
path=`dirname $0`
sleep 1
cd $path
echo "This bash script will create table from ?.stats files"
echo "Written by Jamaan Alghamdi & Dr. Vanessa Sluming"
echo "University of Liverpool"
echo "jamaan.algha...@gmail.com"
echo "http://www.easyneuroimaging.com;
echo "20/12/2010

"


export FREESURFER_HOME=/Applications/freesurfer
sleep 1
source $FREESURFER_HOME/SetUpFreeSurfer.sh
sleep 1

export SUBJECTS_DIR=$PWD
list="`ls -d */`"
asegstats2table --subjects $list --meas volume --skip --statsfile
wmparc.stats --all-segs --tablefile wmparc_stats.txt
.
.
.


I run the script from my_subject_directory.

I suspect this is something very obvious I'm not able to see and I
apologize for such a basic question, any help would be much appreciated.

Thanks,
K
___
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] Cortical surface

[郑凤莲]

External Email - Use Caution

Dear experts,
  I an using FS 6.0 for cortical reconstructions.  I can show whole brain 
regions (tksurfer...), as shown in the picture. However,  I just want to show 
insular region. Is there any way to complete it? I am looking forward to your 
reply. Thanks very much.
Sincerely,
Zheng___
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.