[Freesurfer] Fwd: Regarding: mris_label2annot

[Dr Sampada Sinha]

Dear Freesurfer experts,

I am trying to create medial temporal lobe and for that I ran the command
mri_annotation2label to create ?h.entorhinal.label, ?h.temporalpole.label
and ?h.parahippocampal.label from fsaverage and stored these labels in
labels.?h directory. After this I ran mris_label2annot, taking cue from
page https://surfer.nmr.mgh.harvard.edu/fswiki/mris_label2annot.

My command line is the following (fsaverage has been linked to my subject
directory:

rmbp:AD Sampada$ mris_label2annot  --s fsaverage --h lh --ctab
/Applications/freesurfer/subjects/bert/label/aparc.annot.ctab --a myaparc
--l ./labels_lh/lh.temporalpole.label --l ./labels_lh/lh.parahippocampal.label
--l ./labels_lh/lh.entorhinal.label --nhits nhits.mgh

However, it comes with following error

*Writing annot to
/Users/Sampada/Desktop/AD/fsaverage/label/lh.myaparc.annot*
*could not write annot file
/Users/Sampada/Desktop/AD/fsaverage/label/lh.myaparc.annot*
*Permission denied*

Will you please let me know how to fix this problem . I can see its
a permission error but don't know how to overcome it.

Thanks for your help

Kind regards,

-- 
Sampada
​Research medical scientist (B)​
Department of Geriatric Mental Health (DGMH)
King George Medical University
Lucknow-226003
​, Uttar Pradesh​
India
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Re: [Freesurfer] CUDA in FS6?

[R Edgar]

On 2 February 2017 at 22:58, Chris Adamson  wrote:
> I have tested a recon-all -all CPU and GPU with and without the -hires option 
> and everything seems to run fine. So at the moment they seem to be compatible 
> or at least the GPU version doesn't crash. So that is ok.

If you do come across substantial discrepancies, please let me know,
and I will do my best to resolve them.

Regards,

Richard
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[Freesurfer] Surface based analysis for hippocampus subfield thickness

[Dev vasu]

Dear all,

Is there any approach that you recommend to quantify that changes in
cortical thickness in hippo campus sub fields ,  how could i perform
Surface based cortical thickness changes using freesurfer.

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

[Freesurfer] Perirhinal 6.0 error

[stdp82]

Hi,
by running the mri_label2label to calculate perirhinal morphometry the 
following error occurs with FS6.0ERROR reading sub_DIR/label/rh.perirhinal.label
Thanks

Stefano___
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dispose of the e-mail.

Re: [Freesurfer] license file not working

[Anthony Dick]

Hello,

I got it running. I just deleted all old license files, resent the the 
registration. When I got the email I created both a .license and a 
license.txt in $Freesurfer_Home, and it worked. Just one of those things 
I guess?

Anthony


On 2/3/17 12:34 PM, Z K wrote:
> Anthony,
>
> Is this still an issue for you? So long as there is a license file (name
> .license or license.txt) in the FREESURFER_HOME directory, you should be
> all set.
>
> -Zeke
>
> On 02/02/2017 06:46 PM, Anthony Dick wrote:
>> Thanks Matt. I already tried it with a new registration, but it doesn't
>> hurt to try it again. That may be where the issue is. I'll post if that
>> turns out to be the problem. Thanks!
>>
>> Anthony
>>
>>
>> On 2/2/17 6:28 PM, Matt Glasser wrote:
>>> Like I said, they changed the format at some point and stopped
>>> accepting the old format with FS 6.0.  I have used FreeSurfer for a
>>> long time too and found that I had to get a new license file with this
>>> version.
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> From: >> > on behalf of Anthony
>>> Dick >
>>> Reply-To: Freesurfer support list >> >
>>> Date: Thursday, February 2, 2017 at 5:18 PM
>>> To: >> >
>>> Subject: Re: [Freesurfer] license file not working
>>>
>>> Hello,
>>>
>>> I have used my old file, registered under two different emails (and
>>> received the code and made new files each time, named both .license
>>> and license.txt). Restarted the computer etc. I am wondering if it is
>>> a permissions issue. It seems to be finding the file where I put it.
>>> Have never encountered this issue and have been using Freesurfer for
>>> 11 years. If history is any guide, it will probably turn out to be
>>> something stupid that I did :)
>>>
>>> Anthony
>>>
>>>
>>> On 2/2/17 3:40 PM, Trisanna Sprung-Much wrote:
 The .license that it comes with is not the same as the license.txt
 that you have to acquire. I was able to use an old license.txt from
 my Freesurfer 5.3 for 6.0.

 Best

 Trisanna

 --
 Ph.D. Candidate
 McGill University
 Integrated Program in Neuroscience
 Psychology


 On Thu, Feb 2, 2017 at 3:21 PM, X K > wrote:

  try to rename the file to license.txt?

  On Thu, Feb 2, 2017 at 9:13 PM, Anthony Dick > wrote:

  Hello,

  I have been using Freesurfer for a number of years, and just
  installed
  v6.0. I run into this problem:

  
 --
  ERROR: Invalid FreeSurfer license key found in license file
  /Applications/freesurfer/.license
 If you are outside the NMR-Martinos Center,
 go to http://surfer.nmr.mgh.harvard.edu/registration.html
   to
 get a valid license file (it's free).
 If you are inside the NMR-Martinos Center,
 make sure to source the standard environment.
  
 --

  I have a valid .license file, in the Freesurfer home directory

  Last login: Thu Feb  2 15:04:01 on ttys005
   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  /Applications/freesurfer/subjects
  MNI_DIR   /Applications/freesurfer/mni
  [38c9862eb0b0:~] adick% cd /Applications/freesurfer
  [38c9862eb0b0:/Applications/freesurfer] adick% ls -al .license
  -rw-r--r--  1 root  wheel  140 Feb  2 15:06 .license
  [38c9862eb0b0:/Applications/freesurfer] adick%

  Any ideas?

  Thanks!

  Anthony


  --
  Anthony Steven Dick, Ph.D.
  Associate Professor
  Director, Cognitive Neuroscience Program and Graduate
  Certificate in Cognitive Neuroscience
  Department of Psychology
  Florida International University Modesto A. Maidique Campus
  AHC4 454
  11200 S.W. 8th Street
  Miami, FL 33199
  Ph: 305-348-4202 ; Lab Ph:
  305-348-9055 

Re: [Freesurfer] Probability Maps

[Bruce Fischl]

no, more like:


echo "mri_normalize -b 20" > x.opts

recon-all -s subjectID -autorecon2-cp -autorecon3 -expert x.opts

or if you ware starting from scratch, use your command with the -expert x.opts
stuff at the end

cheers
Bruce

On Fri, 3 
Feb 2017, Pascal Goodman 
wrote:



Thanks bruce. That's
Line 1 recon-all -all -i T2 T2pial -s  subjectID -parallel
Line 2  mri_normalize -mprage -norm2-b 20 -aseg aseg.presurf.mgz -mask 
brainmask.mgz norm.mgz brain.mgz
This is in visual studio code 
 
Cheers, 
Pascal


On Fri, Feb 3, 2017 at 3:45 PM, Bruce Fischl  wrote:
  Hi Pascal

  you can put the

  mri_normalize -b 20

  line in a file, and use it as the expert options in recon-all to rerun 
autorecon2-cp and
  autorecon3 with it

  cheers
  Bruce

  On Fri, 3 Feb 2017, Pascal Goodman wrote:

Thanks bruce. After running mri_normalize -mprage -b 20 -aseg 
aseg.presurf.mgz
-mask brainmask.mgz
norm.mgz brain.mgz, do I need to run recon-all -autorecon2 
-autorecon3
again? Cheer., 
Pascal 

On Fri, Feb 3, 2017 at 2:38 PM, Bruce Fischl 
 wrote:
      Hi Pascal

      yes, that is the right command line. I don't know if you will 
need more
control points, but
      that helped a lot. -a specifies the intensity threshold above 
110 and -g
specifies the
      spatial gradient for the 1d normalization
      cheers
      Bruce

      On Fri, 3 Feb 2017, Pascal Goodman wrote:

            Hello Bruce, Thank you very much.
            a) The mri_normalization command line is where control 
points starts
            (normalization2). Right?
            b) Also, is this right command " mri_normalize -mprage 
-b 20 -aseg
            aseg.presurf.mgz -mask brainmask.mgz
            norm.mgz brain.mgz"?
            c) Do I need any other flag besides -b?
            d) I don't need to make the manual control point edits 
right? 
            e) Lastly, what does -a (float a) and -g (float g) 
mean? 
            Cheers, 
            Pascal

            On Fri, Feb 3, 2017 at 2:14 PM, Bruce Fischl
 wrote:
                  HI Pascal

                  I got significantly improved results using -b 20 
on the
mri_normalize
            command line. Note
                  that this has to come after the mprage. I think 
you can do it
with an
            expert options file
                  with:

                  mri_normalize -b 20

                  cheers
                  Bruce

                  On Fri, 3 Feb 2017, Pascal Goodman wrote:

                        Hello Bruce, I sent it. 
                        Pascal

                        On Fri, Feb 3, 2017 at 11:26 AM, Bruce 
Fischl
            
                        wrote:
                             
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange

                              tar and gzip an example subject 
directory and send
us the
            voxel coords of
                        points you want us
                              to look at

                              cheers
                              Bruce
                              On Fri, 3 Feb 2017, Pascal Goodman 
wrote:

                                    Thanks bruce. Do I upload the 
entire file?
Also,where
            can I find the
                                    link? Pascal

                                    On Fri, Feb 3, 2017 at 10:35 
AM, Bruce
Fischl
                        
                                    wrote:
                                          Hi Pascal

                                          I don't think tissue 
priors will help
due to the
            complexity
                        and
                                    variability of the folding
                                          patterns. There may be 
other
interventions though
            - can you
                        send us some
                                    examples of where
                                          

Re: [Freesurfer] Probability Maps

[Pascal Goodman]

Thanks bruce. That's

Line 1 recon-all -all -i T2 T2pial -s  subjectID -parallel
Line 2  mri_normalize -mprage -norm2-b 20 -aseg aseg.presurf.mgz -mask
brainmask.mgz norm.mgz brain.mgz
This is in visual studio code

Cheers,
Pascal


On Fri, Feb 3, 2017 at 3:45 PM, Bruce Fischl 
wrote:

> Hi Pascal
>
> you can put the
>
> mri_normalize -b 20
>
> line in a file, and use it as the expert options in recon-all to rerun
> autorecon2-cp and autorecon3 with it
>
>
> cheers
> Bruce
>
> On Fri, 3 Feb 2017, Pascal Goodman wrote:
>
> Thanks bruce. After running mri_normalize -mprage -b 20 -aseg
>> aseg.presurf.mgz -mask brainmask.mgz
>> norm.mgz brain.mgz, do I need to run recon-all -autorecon2 -autorecon3
>> again? Cheer.,
>> Pascal
>>
>> On Fri, Feb 3, 2017 at 2:38 PM, Bruce Fischl 
>> wrote:
>>   Hi Pascal
>>
>>   yes, that is the right command line. I don't know if you will need
>> more control points, but
>>   that helped a lot. -a specifies the intensity threshold above 110
>> and -g specifies the
>>   spatial gradient for the 1d normalization
>>   cheers
>>   Bruce
>>
>>   On Fri, 3 Feb 2017, Pascal Goodman wrote:
>>
>> Hello Bruce, Thank you very much.
>> a) The mri_normalization command line is where control points
>> starts
>> (normalization2). Right?
>> b) Also, is this right command " mri_normalize -mprage -b 20
>> -aseg
>> aseg.presurf.mgz -mask brainmask.mgz
>> norm.mgz brain.mgz"?
>> c) Do I need any other flag besides -b?
>> d) I don't need to make the manual control point edits right?
>> e) Lastly, what does -a (float a) and -g (float g) mean?
>> Cheers,
>> Pascal
>>
>> On Fri, Feb 3, 2017 at 2:14 PM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu> wrote:
>>   HI Pascal
>>
>>   I got significantly improved results using -b 20 on the
>> mri_normalize
>> command line. Note
>>   that this has to come after the mprage. I think you can
>> do it with an
>> expert options file
>>   with:
>>
>>   mri_normalize -b 20
>>
>>   cheers
>>   Bruce
>>
>>   On Fri, 3 Feb 2017, Pascal Goodman wrote:
>>
>> Hello Bruce, I sent it.
>> Pascal
>>
>> On Fri, Feb 3, 2017 at 11:26 AM, Bruce Fischl
>> 
>> wrote:
>>   https://surfer.nmr.mgh.harvard
>> .edu/fswiki/FtpFileExchange
>>
>>   tar and gzip an example subject directory
>> and send us the
>> voxel coords of
>> points you want us
>>   to look at
>>
>>   cheers
>>   Bruce
>>   On Fri, 3 Feb 2017, Pascal Goodman wrote:
>>
>> Thanks bruce. Do I upload the entire
>> file? Also,where
>> can I find the
>> link? Pascal
>>
>> On Fri, Feb 3, 2017 at 10:35 AM,
>> Bruce Fischl
>> 
>> wrote:
>>   Hi Pascal
>>
>>   I don't think tissue priors
>> will help due to the
>> complexity
>> and
>> variability of the folding
>>   patterns. There may be other
>> interventions though
>> - can you
>> send us some
>> examples of where
>>   things don't look accurate to
>> you?
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Fri, 3 Feb 2017, Pascal
>> Goodman wrote:
>>
>> Hello Bruce, Thanks for
>> replying. I am
>> trying find ways
>> to improve
>> white matter
>> surface (to reduce
>> manual intervention by
>> control points) with
>> the
>> probability map.
>> Also, how do I
>> extract the multiple
>> prior maps you mentioned.
>> Thank you.
>> Best,
>>

Re: [Freesurfer] Probability Maps

[Bruce Fischl]

Hi Pascal

you can put the

mri_normalize -b 20

line in a file, and use it as the expert options in recon-all to rerun 
autorecon2-cp and autorecon3 with it


cheers
Bruce

On Fri, 3 Feb 2017, Pascal Goodman wrote:


Thanks bruce. After running mri_normalize -mprage -b 20 -aseg aseg.presurf.mgz 
-mask brainmask.mgz
norm.mgz brain.mgz, do I need to run recon-all -autorecon2 -autorecon3 again? 
Cheer., 
Pascal 

On Fri, Feb 3, 2017 at 2:38 PM, Bruce Fischl  wrote:
  Hi Pascal

  yes, that is the right command line. I don't know if you will need more 
control points, but
  that helped a lot. -a specifies the intensity threshold above 110 and -g 
specifies the
  spatial gradient for the 1d normalization
  cheers
  Bruce

  On Fri, 3 Feb 2017, Pascal Goodman wrote:

Hello Bruce, Thank you very much.
a) The mri_normalization command line is where control points starts
(normalization2). Right?
b) Also, is this right command " mri_normalize -mprage -b 20 -aseg
aseg.presurf.mgz -mask brainmask.mgz
norm.mgz brain.mgz"?
c) Do I need any other flag besides -b?
d) I don't need to make the manual control point edits right? 
e) Lastly, what does -a (float a) and -g (float g) mean? 
Cheers, 
Pascal

On Fri, Feb 3, 2017 at 2:14 PM, Bruce Fischl 
 wrote:
      HI Pascal

      I got significantly improved results using -b 20 on the 
mri_normalize
command line. Note
      that this has to come after the mprage. I think you can do it 
with an
expert options file
      with:

      mri_normalize -b 20

      cheers
      Bruce

      On Fri, 3 Feb 2017, Pascal Goodman wrote:

            Hello Bruce, I sent it. 
            Pascal

            On Fri, Feb 3, 2017 at 11:26 AM, Bruce Fischl

            wrote:
                  
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange

                  tar and gzip an example subject directory and 
send us the
voxel coords of
            points you want us
                  to look at

                  cheers
                  Bruce
                  On Fri, 3 Feb 2017, Pascal Goodman wrote:

                        Thanks bruce. Do I upload the entire file? 
Also,where
can I find the
                        link? Pascal

                        On Fri, Feb 3, 2017 at 10:35 AM, Bruce 
Fischl
            
                        wrote:
                              Hi Pascal

                              I don't think tissue priors will help 
due to the
complexity
            and
                        variability of the folding
                              patterns. There may be other 
interventions though
- can you
            send us some
                        examples of where
                              things don't look accurate to you?

                              cheers
                              Bruce


                              On Fri, 3 Feb 2017, Pascal Goodman 
wrote:

                                    Hello Bruce, Thanks for 
replying. I am
trying find ways
            to improve
                        white matter
                                    surface (to reduce
                                    manual intervention by control 
points) with
the
            probability map.
                        Also, how do I
                                    extract the multiple
                                    prior maps you mentioned. Thank 
you. 
                                    Best, 
                                    Pascal

                                    On Fri, Feb 3, 2017 at 10:22 
AM, Bruce
Fischl
                        
                                    wrote:
                                          Hi Pascal

                                          what are you trying to 
achieve?
Internally we have
            multiple
                        prior maps of
                                    this type, but I
                         

Re: [Freesurfer] Probability Maps

[Bruce Fischl]

yes
On Fri, 3 Feb 2017, Pascal Goodman wrote:


Also Bruce, Can I use this command line for the new version of freesurfer " 
mri_normalize -mprage
-norm2-b 20 -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz". 
ThanksPascal. 

On Fri, Feb 3, 2017 at 2:47 PM, Pascal Goodman  wrote:
  Thanks bruce. After running mri_normalize -mprage -b 20 -aseg 
aseg.presurf.mgz -mask
  brainmask.mgz norm.mgz brain.mgz, do I need to run recon-all -autorecon2 
-autorecon3
  again? Cheer., 
Pascal 

On Fri, Feb 3, 2017 at 2:38 PM, Bruce Fischl  wrote:
  Hi Pascal

  yes, that is the right command line. I don't know if you will need more 
control
  points, but that helped a lot. -a specifies the intensity threshold above 
110 and -g
  specifies the spatial gradient for the 1d normalization
  cheers
  Bruce

  On Fri, 3 Feb 2017, Pascal Goodman wrote:

Hello Bruce, Thank you very much.
a) The mri_normalization command line is where control points starts
(normalization2). Right?
b) Also, is this right command " mri_normalize -mprage -b 20 -aseg
aseg.presurf.mgz -mask brainmask.mgz
norm.mgz brain.mgz"?
c) Do I need any other flag besides -b?
d) I don't need to make the manual control point edits right? 
e) Lastly, what does -a (float a) and -g (float g) mean? 
Cheers, 
Pascal

On Fri, Feb 3, 2017 at 2:14 PM, Bruce Fischl 

wrote:
      HI Pascal

      I got significantly improved results using -b 20 on the
mri_normalize command line. Note
      that this has to come after the mprage. I think you can do it 
with
an expert options file
      with:

      mri_normalize -b 20

      cheers
      Bruce

      On Fri, 3 Feb 2017, Pascal Goodman wrote:

            Hello Bruce, I sent it. 
            Pascal

            On Fri, Feb 3, 2017 at 11:26 AM, Bruce Fischl

            wrote:
                 
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange

                  tar and gzip an example subject directory and 
send us
the voxel coords of
            points you want us
                  to look at

                  cheers
                  Bruce
                  On Fri, 3 Feb 2017, Pascal Goodman wrote:

                        Thanks bruce. Do I upload the entire file?
Also,where can I find the
                        link? Pascal

                        On Fri, Feb 3, 2017 at 10:35 AM, Bruce 
Fischl
            
                        wrote:
                              Hi Pascal

                              I don't think tissue priors will help 
due to
the complexity
            and
                        variability of the folding
                              patterns. There may be other 
interventions
though - can you
            send us some
                        examples of where
                              things don't look accurate to you?

                              cheers
                              Bruce


                              On Fri, 3 Feb 2017, Pascal Goodman 
wrote:

                                    Hello Bruce, Thanks for 
replying. I am
trying find ways
            to improve
                        white matter
                                    surface (to reduce
                                    manual intervention by control 
points)
with the
            probability map.
                        Also, how do I
                                    extract the multiple
                                    prior maps you mentioned. Thank 
you. 
                                    Best, 
                                    Pascal

                                    On Fri, Feb 3, 2017 at 10:22 
AM, Bruce
Fischl
                        
                                    wrote:
                                          Hi Pascal

                                          what are you trying to 
achieve?
Internally we have
            multiple
   

Re: [Freesurfer] Probability Maps

[Pascal Goodman]

Also Bruce, Can I use this command line for the new version of freesurfer "
mri_normalize -mprage -norm2-b 20 -aseg aseg.presurf.mgz -mask
brainmask.mgz norm.mgz brain.mgz". Thanks
Pascal.

On Fri, Feb 3, 2017 at 2:47 PM, Pascal Goodman  wrote:

> Thanks bruce. After running mri_normalize -mprage -b 20 -aseg
> aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz, do I need to run
> recon-all -autorecon2 -autorecon3 again?
> Cheer.,
> Pascal
>
> On Fri, Feb 3, 2017 at 2:38 PM, Bruce Fischl 
> wrote:
>
>> Hi Pascal
>>
>> yes, that is the right command line. I don't know if you will need more
>> control points, but that helped a lot. -a specifies the intensity threshold
>> above 110 and -g specifies the spatial gradient for the 1d normalization
>>
>> cheers
>> Bruce
>>
>> On Fri, 3 Feb 2017, Pascal Goodman wrote:
>>
>> Hello Bruce, Thank you very much.
>>> a) The mri_normalization command line is where control points starts
>>> (normalization2). Right?
>>> b) Also, is this right command " mri_normalize -mprage -b 20 -aseg
>>> aseg.presurf.mgz -mask brainmask.mgz
>>> norm.mgz brain.mgz"?
>>> c) Do I need any other flag besides -b?
>>> d) I don't need to make the manual control point edits right?
>>> e) Lastly, what does -a (float a) and -g (float g) mean?
>>> Cheers,
>>> Pascal
>>>
>>> On Fri, Feb 3, 2017 at 2:14 PM, Bruce Fischl 
>>> wrote:
>>>   HI Pascal
>>>
>>>   I got significantly improved results using -b 20 on the
>>> mri_normalize command line. Note
>>>   that this has to come after the mprage. I think you can do it with
>>> an expert options file
>>>   with:
>>>
>>>   mri_normalize -b 20
>>>
>>>   cheers
>>>   Bruce
>>>
>>>   On Fri, 3 Feb 2017, Pascal Goodman wrote:
>>>
>>> Hello Bruce, I sent it.
>>> Pascal
>>>
>>> On Fri, Feb 3, 2017 at 11:26 AM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu>
>>> wrote:
>>>   https://surfer.nmr.mgh.harvard
>>> .edu/fswiki/FtpFileExchange
>>>
>>>   tar and gzip an example subject directory and send us
>>> the voxel coords of
>>> points you want us
>>>   to look at
>>>
>>>   cheers
>>>   Bruce
>>>   On Fri, 3 Feb 2017, Pascal Goodman wrote:
>>>
>>> Thanks bruce. Do I upload the entire file?
>>> Also,where can I find the
>>> link? Pascal
>>>
>>> On Fri, Feb 3, 2017 at 10:35 AM, Bruce Fischl
>>> 
>>> wrote:
>>>   Hi Pascal
>>>
>>>   I don't think tissue priors will help due
>>> to the complexity
>>> and
>>> variability of the folding
>>>   patterns. There may be other interventions
>>> though - can you
>>> send us some
>>> examples of where
>>>   things don't look accurate to you?
>>>
>>>   cheers
>>>   Bruce
>>>
>>>
>>>   On Fri, 3 Feb 2017, Pascal Goodman wrote:
>>>
>>> Hello Bruce, Thanks for replying. I
>>> am trying find ways
>>> to improve
>>> white matter
>>> surface (to reduce
>>> manual intervention by control
>>> points) with the
>>> probability map.
>>> Also, how do I
>>> extract the multiple
>>> prior maps you mentioned. Thank you.
>>> Best,
>>> Pascal
>>>
>>> On Fri, Feb 3, 2017 at 10:22 AM,
>>> Bruce Fischl
>>> 
>>> wrote:
>>>   Hi Pascal
>>>
>>>   what are you trying to
>>> achieve? Internally we have
>>> multiple
>>> prior maps of
>>> this type, but I
>>>   don't think we are setup for a
>>> user to supply a
>>> different one
>>>
>>>   cheers
>>>   Bruce
>>>
>>>   On Fri, 3 Feb 2017, Pascal
>>> Goodman wrote:
>>>
>>> Hello Freesurfer, I do
>>> have a question. Can
>>> FS take
>>> probability maps
>>> of  tissue
>>>

Re: [Freesurfer] Probability Maps

[Pascal Goodman]

Thanks bruce. After running mri_normalize -mprage -b 20 -aseg
aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz, do I need to run
recon-all -autorecon2 -autorecon3 again?
Cheer.,
Pascal

On Fri, Feb 3, 2017 at 2:38 PM, Bruce Fischl 
wrote:

> Hi Pascal
>
> yes, that is the right command line. I don't know if you will need more
> control points, but that helped a lot. -a specifies the intensity threshold
> above 110 and -g specifies the spatial gradient for the 1d normalization
>
> cheers
> Bruce
>
> On Fri, 3 Feb 2017, Pascal Goodman wrote:
>
> Hello Bruce, Thank you very much.
>> a) The mri_normalization command line is where control points starts
>> (normalization2). Right?
>> b) Also, is this right command " mri_normalize -mprage -b 20 -aseg
>> aseg.presurf.mgz -mask brainmask.mgz
>> norm.mgz brain.mgz"?
>> c) Do I need any other flag besides -b?
>> d) I don't need to make the manual control point edits right?
>> e) Lastly, what does -a (float a) and -g (float g) mean?
>> Cheers,
>> Pascal
>>
>> On Fri, Feb 3, 2017 at 2:14 PM, Bruce Fischl 
>> wrote:
>>   HI Pascal
>>
>>   I got significantly improved results using -b 20 on the
>> mri_normalize command line. Note
>>   that this has to come after the mprage. I think you can do it with
>> an expert options file
>>   with:
>>
>>   mri_normalize -b 20
>>
>>   cheers
>>   Bruce
>>
>>   On Fri, 3 Feb 2017, Pascal Goodman wrote:
>>
>> Hello Bruce, I sent it.
>> Pascal
>>
>> On Fri, Feb 3, 2017 at 11:26 AM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> wrote:
>>   https://surfer.nmr.mgh.harvard
>> .edu/fswiki/FtpFileExchange
>>
>>   tar and gzip an example subject directory and send us
>> the voxel coords of
>> points you want us
>>   to look at
>>
>>   cheers
>>   Bruce
>>   On Fri, 3 Feb 2017, Pascal Goodman wrote:
>>
>> Thanks bruce. Do I upload the entire file?
>> Also,where can I find the
>> link? Pascal
>>
>> On Fri, Feb 3, 2017 at 10:35 AM, Bruce Fischl
>> 
>> wrote:
>>   Hi Pascal
>>
>>   I don't think tissue priors will help due
>> to the complexity
>> and
>> variability of the folding
>>   patterns. There may be other interventions
>> though - can you
>> send us some
>> examples of where
>>   things don't look accurate to you?
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Fri, 3 Feb 2017, Pascal Goodman wrote:
>>
>> Hello Bruce, Thanks for replying. I
>> am trying find ways
>> to improve
>> white matter
>> surface (to reduce
>> manual intervention by control
>> points) with the
>> probability map.
>> Also, how do I
>> extract the multiple
>> prior maps you mentioned. Thank you.
>> Best,
>> Pascal
>>
>> On Fri, Feb 3, 2017 at 10:22 AM,
>> Bruce Fischl
>> 
>> wrote:
>>   Hi Pascal
>>
>>   what are you trying to achieve?
>> Internally we have
>> multiple
>> prior maps of
>> this type, but I
>>   don't think we are setup for a
>> user to supply a
>> different one
>>
>>   cheers
>>   Bruce
>>
>>   On Fri, 3 Feb 2017, Pascal
>> Goodman wrote:
>>
>> Hello Freesurfer, I do
>> have a question. Can
>> FS take
>> probability maps
>> of  tissue
>> segmentation as prior?
>> Thanks,
>> Pascal
>>
>>
>>
>> __
>> _
>> Freesurfer mailing list
>> 

Re: [Freesurfer] Probability Maps

[Bruce Fischl]

Hi Pascal

yes, that is the right command line. I don't know if you will need more 
control points, but that helped a lot. -a specifies the intensity threshold 
above 110 and -g specifies the spatial gradient for the 1d normalization

cheers
Bruce

On Fri, 3 Feb 
2017, Pascal Goodman wrote:



Hello Bruce, Thank you very much.
a) The mri_normalization command line is where control points starts 
(normalization2). Right?
b) Also, is this right command " mri_normalize -mprage -b 20 -aseg 
aseg.presurf.mgz -mask brainmask.mgz
norm.mgz brain.mgz"?
c) Do I need any other flag besides -b?
d) I don't need to make the manual control point edits right? 
e) Lastly, what does -a (float a) and -g (float g) mean? 
Cheers, 
Pascal

On Fri, Feb 3, 2017 at 2:14 PM, Bruce Fischl  wrote:
  HI Pascal

  I got significantly improved results using -b 20 on the mri_normalize 
command line. Note
  that this has to come after the mprage. I think you can do it with an 
expert options file
  with:

  mri_normalize -b 20

  cheers
  Bruce

  On Fri, 3 Feb 2017, Pascal Goodman wrote:

Hello Bruce, I sent it. 
Pascal

On Fri, Feb 3, 2017 at 11:26 AM, Bruce Fischl 

wrote:
      https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange

      tar and gzip an example subject directory and send us the 
voxel coords of
points you want us
      to look at

      cheers
      Bruce
      On Fri, 3 Feb 2017, Pascal Goodman wrote:

            Thanks bruce. Do I upload the entire file? Also,where 
can I find the
            link? Pascal

            On Fri, Feb 3, 2017 at 10:35 AM, Bruce Fischl

            wrote:
                  Hi Pascal

                  I don't think tissue priors will help due to the 
complexity
and
            variability of the folding
                  patterns. There may be other interventions though 
- can you
send us some
            examples of where
                  things don't look accurate to you?

                  cheers
                  Bruce


                  On Fri, 3 Feb 2017, Pascal Goodman wrote:

                        Hello Bruce, Thanks for replying. I am 
trying find ways
to improve
            white matter
                        surface (to reduce
                        manual intervention by control points) with 
the
probability map.
            Also, how do I
                        extract the multiple
                        prior maps you mentioned. Thank you. 
                        Best, 
                        Pascal

                        On Fri, Feb 3, 2017 at 10:22 AM, Bruce 
Fischl
            
                        wrote:
                              Hi Pascal

                              what are you trying to achieve? 
Internally we have
multiple
            prior maps of
                        this type, but I
                              don't think we are setup for a user 
to supply a
different one

                              cheers
                              Bruce

                              On Fri, 3 Feb 2017, Pascal Goodman 
wrote:

                                    Hello Freesurfer, I do have a 
question. Can
FS take
            probability maps
                        of  tissue
                                    segmentation as prior? 
                                    Thanks, 
                                    Pascal



                        
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[Freesurfer] Whole brain mediation analysis

[Michael Kranz]

Hi,

I was wondering if you guys had any suggestions for developing a whole
brain mediation analysis through Freesurfer or can think of any examples
(e.g., does thickness mediate the relationship between age and cognition)?

It looks like SPM has something (whole brain mediation analysis), and given
the outputs from mri_glmfit, it seems like it would be possible with
Freesurfer.

Best,
Mike

-- 
Michael Kranz
Graduate Research Assistant | Beckman Institute University of Illinois
314-323-1329
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Re: [Freesurfer] Probability Maps

[Pascal Goodman]

Hello Bruce,
Thank you very much.
a) The mri_normalization command line is where control points starts
(normalization2). Right?
b) Also, is this right command " mri_normalize
 -mprage -b 20
-aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz"?
c) Do I need any other flag besides -b?
d) I don't need to make the manual control point edits right?
e) Lastly, what does -a (float a) and -g (float g) mean?
Cheers,
Pascal

On Fri, Feb 3, 2017 at 2:14 PM, Bruce Fischl 
wrote:

> HI Pascal
>
> I got significantly improved results using -b 20 on the mri_normalize
> command line. Note that this has to come after the mprage. I think you can
> do it with an expert options file with:
>
> mri_normalize -b 20
>
>
> cheers
> Bruce
>
> On Fri, 3 Feb 2017, Pascal Goodman wrote:
>
> Hello Bruce, I sent it.
>> Pascal
>>
>> On Fri, Feb 3, 2017 at 11:26 AM, Bruce Fischl 
>> wrote:
>>   https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
>>
>>   tar and gzip an example subject directory and send us the voxel
>> coords of points you want us
>>   to look at
>>
>>   cheers
>>   Bruce
>>   On Fri, 3 Feb 2017, Pascal Goodman wrote:
>>
>> Thanks bruce. Do I upload the entire file? Also,where can I
>> find the
>> link? Pascal
>>
>> On Fri, Feb 3, 2017 at 10:35 AM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> wrote:
>>   Hi Pascal
>>
>>   I don't think tissue priors will help due to the
>> complexity and
>> variability of the folding
>>   patterns. There may be other interventions though - can
>> you send us some
>> examples of where
>>   things don't look accurate to you?
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Fri, 3 Feb 2017, Pascal Goodman wrote:
>>
>> Hello Bruce, Thanks for replying. I am trying
>> find ways to improve
>> white matter
>> surface (to reduce
>> manual intervention by control points) with the
>> probability map.
>> Also, how do I
>> extract the multiple
>> prior maps you mentioned. Thank you.
>> Best,
>> Pascal
>>
>> On Fri, Feb 3, 2017 at 10:22 AM, Bruce Fischl
>> 
>> wrote:
>>   Hi Pascal
>>
>>   what are you trying to achieve? Internally
>> we have multiple
>> prior maps of
>> this type, but I
>>   don't think we are setup for a user to
>> supply a different one
>>
>>   cheers
>>   Bruce
>>
>>   On Fri, 3 Feb 2017, Pascal Goodman wrote:
>>
>> Hello Freesurfer, I do have a
>> question. Can FS take
>> probability maps
>> of  tissue
>> segmentation as prior?
>> Thanks,
>> Pascal
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.e
>> du/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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>> 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 

Re: [Freesurfer] Probability Maps

[Bruce Fischl]

HI Pascal

I got significantly improved results using -b 20 on the mri_normalize 
command line. Note that this has to come after the mprage. I think you can 
do it with an expert options file with:


mri_normalize -b 20

cheers
Bruce

On Fri, 3 Feb 2017, Pascal Goodman wrote:


Hello Bruce, I sent it. 
Pascal

On Fri, Feb 3, 2017 at 11:26 AM, Bruce Fischl  
wrote:
  https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange

  tar and gzip an example subject directory and send us the voxel coords of 
points you want us
  to look at

  cheers
  Bruce
  On Fri, 3 Feb 2017, Pascal Goodman wrote:

Thanks bruce. Do I upload the entire file? Also,where can I find the
link? Pascal

On Fri, Feb 3, 2017 at 10:35 AM, Bruce Fischl 

wrote:
      Hi Pascal

      I don't think tissue priors will help due to the complexity 
and
variability of the folding
      patterns. There may be other interventions though - can you 
send us some
examples of where
      things don't look accurate to you?

      cheers
      Bruce


      On Fri, 3 Feb 2017, Pascal Goodman wrote:

            Hello Bruce, Thanks for replying. I am trying find ways 
to improve
white matter
            surface (to reduce
            manual intervention by control points) with the 
probability map.
Also, how do I
            extract the multiple
            prior maps you mentioned. Thank you. 
            Best, 
            Pascal

            On Fri, Feb 3, 2017 at 10:22 AM, Bruce Fischl

            wrote:
                  Hi Pascal

                  what are you trying to achieve? Internally we 
have multiple
prior maps of
            this type, but I
                  don't think we are setup for a user to supply a 
different one

                  cheers
                  Bruce

                  On Fri, 3 Feb 2017, Pascal Goodman wrote:

                        Hello Freesurfer, I do have a question. Can 
FS take
probability maps
            of  tissue
                        segmentation as prior? 
                        Thanks, 
                        Pascal



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Re: [Freesurfer] Kind Request - Trouble with FreeSurfer LICENSE file

[Z K]

The LICENSE file contained in the freesurfer release is a Software 
License Agreement and has nothing to do with the license file required 
to run the freesurfer program.

To get a license file, please go to our registration page and a license 
will be emailed to you. Just copy the correct portion of text into a 
file called .license or license.txt and place it into your 
FREESURFER_HOME directory. Hope this helps.

   https://surfer.nmr.mgh.harvard.edu/registration.html

-Zeke

On 02/03/2017 02:03 PM, Abhinav Kurada wrote:
> To Whom It May Concern:
>
> I am currently unable to successfuly register my copy of FreeSurfer with
> the license keys I received. Although I found a LICENSE file in the
> FreeSurfer program directory after successfully installing the program,
> I could not find the CUT Here lines as well as the location of placing
> the text emailed to me.
>
> Could you please assist me in helping register my copy of FreeSurfer?
>
> Thank you in advance.
>
> Sincerely,
>
> Abhinav Kurada
> Columbia University
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Kind Request - Trouble with FreeSurfer LICENSE file

[Abhinav Kurada]

To Whom It May Concern:

I am currently unable to successfuly register my copy of FreeSurfer with the 
license keys I received. Although I found a LICENSE file in the FreeSurfer 
program directory after successfully installing the program, I could not find 
the CUT Here lines as well as the location of placing the text emailed to me. 

Could you please assist me in helping register my copy of FreeSurfer?

Thank you in advance.

Sincerely,

Abhinav Kurada

Columbia University___
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Re: [Freesurfer] license file not working

[Matt Glasser]

No worries Bruce!

Matt.

On 2/3/17, 12:52 PM, "Bruce Fischl"
 wrote:

>Hi Matt
>
>just to clarify - our old license format stopped working with newer
>versions of libcrypt and so we were forced to change to the new format.
>It 
>was not done gratuitously on our part or as a way to get people to
>request 
>new licenses - we had no choice.
>
>cheers
>Bruce
>
>
>On Thu, 2 Feb 2017, Matt Glasser wrote:
>
>> Like I said, they changed the format at some point and stopped
>>accepting the old format with FS 6.0.  I
>> have used FreeSurfer for a long time too and found that I had to get a
>>new license file with this
>> version.
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From:  on behalf of Anthony
>>Dick 
>> Reply-To: Freesurfer support list 
>> Date: Thursday, February 2, 2017 at 5:18 PM
>> To: 
>> Subject: Re: [Freesurfer] license file not working
>> 
>> Hello,
>> 
>> I have used my old file, registered under two different emails (and
>>received the code and made new files
>> each time, named both .license and license.txt). Restarted the computer
>>etc. I am wondering if it is a
>> permissions issue. It seems to be finding the file where I put it. Have
>>never encountered this issue and
>> have been using Freesurfer for 11 years. If history is any guide, it
>>will probably turn out to be
>> something stupid that I did :)
>> 
>> Anthony
>> 
>> 
>> On 2/2/17 3:40 PM, Trisanna Sprung-Much wrote:
>>   The .license that it comes with is not the same as the
>>license.txt that you have to acquire.
>>   I was able to use an old license.txt from my Freesurfer 5.3 for
>>6.0.
>> Best
>> 
>> Trisanna
>> 
>> --
>> Ph.D. Candidate McGill University
>> Integrated Program in Neuroscience
>> Psychology
>> 
>> 
>> On Thu, Feb 2, 2017 at 3:21 PM, X K  wrote:
>>   try to rename the file to license.txt?
>> 
>> On Thu, Feb 2, 2017 at 9:13 PM, Anthony Dick  wrote:
>>   Hello,
>>
>>   I have been using Freesurfer for a number of years, and just
>>installed
>>   v6.0. I run into this problem:
>>
>>   
>>-
>>-
>>   ERROR: Invalid FreeSurfer license key found in license file
>>   /Applications/freesurfer/.license
>>  If you are outside the NMR-Martinos Center,
>>  go to http://surfer.nmr.mgh.harvard.edu/registration.html to
>>  get a valid license file (it's free).
>>  If you are inside the NMR-Martinos Center,
>>  make sure to source the standard environment.
>>   
>>-
>>-
>>
>>   I have a valid .license file, in the Freesurfer home directory
>>
>>   Last login: Thu Feb  2 15:04:01 on ttys005
>>    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  /Applications/freesurfer/subjects
>>   MNI_DIR   /Applications/freesurfer/mni
>>   [38c9862eb0b0:~] adick% cd /Applications/freesurfer
>>   [38c9862eb0b0:/Applications/freesurfer] adick% ls -al .license
>>   -rw-r--r--  1 root  wheel  140 Feb  2 15:06 .license
>>   [38c9862eb0b0:/Applications/freesurfer] adick%
>>
>>   Any ideas?
>>
>>   Thanks!
>>
>>   Anthony
>> 
>>
>>   --
>>   Anthony Steven Dick, Ph.D.
>>   Associate Professor
>>   Director, Cognitive Neuroscience Program and Graduate Certificate
>>in Cognitive
>>   Neuroscience
>>   Department of Psychology
>>   Florida International University Modesto A. Maidique Campus AHC4
>>454
>>   11200 S.W. 8th Street
>>   Miami, FL 33199
>>   Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
>>   Email: ad...@fiu.edu
>>   Webpage: http://myweb.fiu.edu/adick
>>   Join the Society for the Study of Human Development:
>>http://www.sshdonline.org
>>
>>   ___
>>   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] license file not working

[Bruce Fischl]

Hi Matt

just to clarify - our old license format stopped working with newer 
versions of libcrypt and so we were forced to change to the new format. It 
was not done gratuitously on our part or as a way to get people to request 
new licenses - we had no choice.


cheers
Bruce


On Thu, 2 Feb 2017, Matt Glasser wrote:


Like I said, they changed the format at some point and stopped accepting the 
old format with FS 6.0.  I
have used FreeSurfer for a long time too and found that I had to get a new 
license file with this
version.

Peace,

Matt.

From:  on behalf of Anthony Dick 

Reply-To: Freesurfer support list 
Date: Thursday, February 2, 2017 at 5:18 PM
To: 
Subject: Re: [Freesurfer] license file not working

Hello,

I have used my old file, registered under two different emails (and received 
the code and made new files
each time, named both .license and license.txt). Restarted the computer etc. I 
am wondering if it is a
permissions issue. It seems to be finding the file where I put it. Have never 
encountered this issue and
have been using Freesurfer for 11 years. If history is any guide, it will 
probably turn out to be
something stupid that I did :)

Anthony


On 2/2/17 3:40 PM, Trisanna Sprung-Much wrote:
  The .license that it comes with is not the same as the license.txt that 
you have to acquire.
  I was able to use an old license.txt from my Freesurfer 5.3 for 6.0.
Best

Trisanna

--
Ph.D. Candidate McGill University
Integrated Program in Neuroscience
Psychology


On Thu, Feb 2, 2017 at 3:21 PM, X K  wrote:
  try to rename the file to license.txt?

On Thu, Feb 2, 2017 at 9:13 PM, Anthony Dick  wrote:
  Hello,

  I have been using Freesurfer for a number of years, and just installed
  v6.0. I run into this problem:

  --
  ERROR: Invalid FreeSurfer license key found in license file
  /Applications/freesurfer/.license
     If you are outside the NMR-Martinos Center,
     go to http://surfer.nmr.mgh.harvard.edu/registration.html to
     get a valid license file (it's free).
     If you are inside the NMR-Martinos Center,
     make sure to source the standard environment.
  --

  I have a valid .license file, in the Freesurfer home directory

  Last login: Thu Feb  2 15:04:01 on ttys005
   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      /Applications/freesurfer/subjects
  MNI_DIR           /Applications/freesurfer/mni
  [38c9862eb0b0:~] adick% cd /Applications/freesurfer
  [38c9862eb0b0:/Applications/freesurfer] adick% ls -al .license
  -rw-r--r--  1 root  wheel  140 Feb  2 15:06 .license
  [38c9862eb0b0:/Applications/freesurfer] adick%

  Any ideas?

  Thanks!

  Anthony


  --
  Anthony Steven Dick, Ph.D.
  Associate Professor
  Director, Cognitive Neuroscience Program and Graduate Certificate in 
Cognitive
  Neuroscience
  Department of Psychology
  Florida International University Modesto A. Maidique Campus AHC4 454
  11200 S.W. 8th Street
  Miami, FL 33199
  Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
  Email: ad...@fiu.edu
  Webpage: http://myweb.fiu.edu/adick
  Join the Society for the Study of Human Development: 
http://www.sshdonline.org

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




--
-
Kong Xiangzhen
State Key Laboratory of Cognitive Neuroscience and Learning,
Beijing Normal University,
Beijing, China, 100875.

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addressed. If you believe this e-mail was sent to you in 

Re: [Freesurfer] Probability Maps

[Pascal Goodman]

Hello Bruce,
I sent it.
Pascal

On Fri, Feb 3, 2017 at 11:26 AM, Bruce Fischl 
wrote:

> https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
>
> tar and gzip an example subject directory and send us the voxel coords of
> points you want us to look at
>
>
> cheers
> Bruce
> On Fri, 3 Feb 2017, Pascal Goodman wrote:
>
> Thanks bruce. Do I upload the entire file? Also,where can I find the
>> link? Pascal
>>
>> On Fri, Feb 3, 2017 at 10:35 AM, Bruce Fischl 
>> wrote:
>>   Hi Pascal
>>
>>   I don't think tissue priors will help due to the complexity and
>> variability of the folding
>>   patterns. There may be other interventions though - can you send us
>> some examples of where
>>   things don't look accurate to you?
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Fri, 3 Feb 2017, Pascal Goodman wrote:
>>
>> Hello Bruce, Thanks for replying. I am trying find ways to
>> improve white matter
>> surface (to reduce
>> manual intervention by control points) with the probability
>> map. Also, how do I
>> extract the multiple
>> prior maps you mentioned. Thank you.
>> Best,
>> Pascal
>>
>> On Fri, Feb 3, 2017 at 10:22 AM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> wrote:
>>   Hi Pascal
>>
>>   what are you trying to achieve? Internally we have
>> multiple prior maps of
>> this type, but I
>>   don't think we are setup for a user to supply a
>> different one
>>
>>   cheers
>>   Bruce
>>
>>   On Fri, 3 Feb 2017, Pascal Goodman wrote:
>>
>> Hello Freesurfer, I do have a question. Can FS
>> take probability maps
>> of  tissue
>> segmentation as prior?
>> Thanks,
>> Pascal
>>
>>
>>
>> ___
>> 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.
>>
>>
>>
>>
> ___
> 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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[Freesurfer] A note about the Freesurfer license file

[Z K]

Hello All,

Users on newer linux distributions who upgrade from Freesurfer version 
5.3 to version 6.0 may get the following error message:

--
GNU libc version: 2.17
ERROR: Systems running GNU glibc version greater than 2.15
   require a newly formatted license file (it's free). Please
   download a new one from the following page:
   http://surfer.nmr.mgh.harvard.edu/registration.html
--

This is a known issue, and as the message says, it is resolved by 
downloading a newly formatted license file from our registration page:

   http://surfer.nmr.mgh.harvard.edu/registration.html

Simply overwrite the old license file with the newly formatted one. 
Sorry for any inconvenience this may have caused.

-The Freesurfer team
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dispose of the e-mail.

Re: [Freesurfer] license file not working

[Z K]

Anthony,

Is this still an issue for you? So long as there is a license file (name 
.license or license.txt) in the FREESURFER_HOME directory, you should be 
all set.

-Zeke

On 02/02/2017 06:46 PM, Anthony Dick wrote:
> Thanks Matt. I already tried it with a new registration, but it doesn't
> hurt to try it again. That may be where the issue is. I'll post if that
> turns out to be the problem. Thanks!
>
> Anthony
>
>
> On 2/2/17 6:28 PM, Matt Glasser wrote:
>> Like I said, they changed the format at some point and stopped
>> accepting the old format with FS 6.0.  I have used FreeSurfer for a
>> long time too and found that I had to get a new license file with this
>> version.
>>
>> Peace,
>>
>> Matt.
>>
>> From: > > on behalf of Anthony
>> Dick >
>> Reply-To: Freesurfer support list > >
>> Date: Thursday, February 2, 2017 at 5:18 PM
>> To: > >
>> Subject: Re: [Freesurfer] license file not working
>>
>> Hello,
>>
>> I have used my old file, registered under two different emails (and
>> received the code and made new files each time, named both .license
>> and license.txt). Restarted the computer etc. I am wondering if it is
>> a permissions issue. It seems to be finding the file where I put it.
>> Have never encountered this issue and have been using Freesurfer for
>> 11 years. If history is any guide, it will probably turn out to be
>> something stupid that I did :)
>>
>> Anthony
>>
>>
>> On 2/2/17 3:40 PM, Trisanna Sprung-Much wrote:
>>> The .license that it comes with is not the same as the license.txt
>>> that you have to acquire. I was able to use an old license.txt from
>>> my Freesurfer 5.3 for 6.0.
>>>
>>> Best
>>>
>>> Trisanna
>>>
>>> --
>>> Ph.D. Candidate
>>> McGill University
>>> Integrated Program in Neuroscience
>>> Psychology
>>>
>>>
>>> On Thu, Feb 2, 2017 at 3:21 PM, X K >> > wrote:
>>>
>>> try to rename the file to license.txt?
>>>
>>> On Thu, Feb 2, 2017 at 9:13 PM, Anthony Dick >> > wrote:
>>>
>>> Hello,
>>>
>>> I have been using Freesurfer for a number of years, and just
>>> installed
>>> v6.0. I run into this problem:
>>>
>>> 
>>> --
>>> ERROR: Invalid FreeSurfer license key found in license file
>>> /Applications/freesurfer/.license
>>>If you are outside the NMR-Martinos Center,
>>>go to http://surfer.nmr.mgh.harvard.edu/registration.html
>>>  to
>>>get a valid license file (it's free).
>>>If you are inside the NMR-Martinos Center,
>>>make sure to source the standard environment.
>>> 
>>> --
>>>
>>> I have a valid .license file, in the Freesurfer home directory
>>>
>>> Last login: Thu Feb  2 15:04:01 on ttys005
>>>  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  /Applications/freesurfer/subjects
>>> MNI_DIR   /Applications/freesurfer/mni
>>> [38c9862eb0b0:~] adick% cd /Applications/freesurfer
>>> [38c9862eb0b0:/Applications/freesurfer] adick% ls -al .license
>>> -rw-r--r--  1 root  wheel  140 Feb  2 15:06 .license
>>> [38c9862eb0b0:/Applications/freesurfer] adick%
>>>
>>> Any ideas?
>>>
>>> Thanks!
>>>
>>> Anthony
>>>
>>>
>>> --
>>> Anthony Steven Dick, Ph.D.
>>> Associate Professor
>>> Director, Cognitive Neuroscience Program and Graduate
>>> Certificate in Cognitive Neuroscience
>>> Department of Psychology
>>> Florida International University Modesto A. Maidique Campus
>>> AHC4 454
>>> 11200 S.W. 8th Street
>>> Miami, FL 33199
>>> Ph: 305-348-4202 ; Lab Ph:
>>> 305-348-9055 ; Fx: 305-348-3879
>>> 
>>> Email: ad...@fiu.edu 
>>> Webpage: http://myweb.fiu.edu/adick
>>> Join the Society for the Study of Human Development:
>>> http://www.sshdonline.org
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> 

Re: [Freesurfer] Multiple comparison question

[neuroimage analyst]

Thank you, Anderson.

Regards.

VM

On Thu, Feb 2, 2017 at 11:06 PM, Anderson M. Winkler  wrote:

> Hi VM,
>
> They can stay all in the same .csv file. The "fwep" files will have
> p-values corrected across all columns of this input.
>
> All the best,
>
> Anderson
>
>
> On 2 February 2017 at 12:09, neuroimage analyst <
> neuroimage.anal...@gmail.com> wrote:
>
>> Thanks, Anderson. If there are several other measures such as volume,
>> thickness, FA,  can I then put them in a single csv file and run the
>> command or I have to create 3 csv files, one each for volume, thickness,and
>> FA and also invoke -corrmod?
>>
>> Thanks
>>
>> Regards
>> VM
>>
>> On Feb 2, 2017 1:01 AM, "Anderson M. Winkler" 
>> wrote:
>>
>> Hi VM,
>>
>> Please see below:
>>
>>
>> On 1 February 2017 at 02:38, neuroimage analyst <
>> neuroimage.anal...@gmail.com> wrote:
>>
>>> Hi,
>>>
>>> We extracted volume measures from 7 ROIs in 2 groups and compared
>>> a) Mean of each ROI volume between group, and compared independently
>>> such as
>>> i) whether mean of ROI 1 in group 1 is equal to mean of ROI1 in group 2
>>> ii)whether mean of ROI 2 in group 1 is equal to mean of ROI2 in group 2
>>>  and so on
>>>
>>
>> This means 7 comparisons, or 14 if you test both directions (tails)
>> separately.
>>
>>
>>>
>>> b) Plotted the mean ROI volume for 2 independent measures and compared
>>> whether the slope between and within group is significantly different. such
>>> as
>>> i) Slope of ROI1 is positively associated with MoCA , age (grp1) ?
>>> ii) Slope of ROI1 is negatively associated with MoCA, age (grp2) ?
>>> iii) Slope of ROI1 vs MoCA (grp1) is significantly different
>>> than slope of ROI1 vs MoCA (grp2) ?
>>> iv) Slope of ROI1 vs MoCA (grp2) is significantly different
>>> than slope of ROI2 vs MoCA (grp2) ?
>>>
>>
>> These sound tests for main effects and interaction, with various
>> combinations possible.
>>
>>
>>>
>>> Q1) Do we have to perform multiple comparisons for (a) and (b)?
>>>
>>
>> Yes.
>>
>>
>>
>>> Q2) If yes, do we correct across 7 measurements for (a) and 2
>>> measurements for (b) or 7 measurements for both (a) and (b)?
>>>
>>
>> You could put the values for the 7 ROIs in a table in .csv format, with
>> one column per ROI and one row per subject. This would be the input data.
>> Create a design matrix as:
>>
>> EV1: 0 or 1 coding for group 1
>> EV2: 0 or 1 coding for group 2
>> EV3: MoCA group 1
>> EV4: MoCA group 2
>> EV5: Age group 1
>> EV6: Age group 2
>> etc
>>
>> Then define a set of contrasts such as:
>>
>> C1: [1 -1 0 0 0 0 ...] - This tests if mean for group 1 > mean for group 2
>> C2: [-1 1 0 0 0 0 ...] - This tests if mean for group 1 < mean for group 2
>> C3: [0 0 1 -1 0 0 ...] - This tests if the slope for MoCA for group 1 >
>> slope for MoCA for group 2
>> C4: [0 0 -1 1 0 0 ...] - This tests if the slope for MoCA for group 1 <
>> slope for MoCA for group 2
>> C5: [0 0 1 0 0 0 ...] - This tests if slope for MoCA for group 1 > 0
>> C6: [0 0 -1 0 0 0 ...] - This tests if slope for MoCA for group 1 < 0
>> etc
>>
>> You'd run this analysis in PALM with something as:
>>
>> *palm -i input.csv -d design.mat -t design.con -corrcon -o myresults
>> -logp*
>>
>>
>> Hope this helps!
>>
>> All the best,
>>
>> Anderson
>>
>>
>>
>>> There is evidence to both performing and nonperforming multiple
>>> comparisons In the literature.
>>>
>>> Any response (hopefully pointing to a literature) will be greatly
>>> appreciated.
>>>
>>> Thanks
>>>
>>> Regards
>>>
>>> --VM
>>>
>>> ___
>>> Freesurfer mailing list
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>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>> in error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>>
>>>
>>
>> ___
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>>
>>
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Re: [Freesurfer] how to export cortical thickness in to .txt

[Bruce Fischl]

Hi shi yao

if you have run recon-all then we have already done this for you. Look in 
the subject's stats dir (that is, $SUBJECTS_DIR/$subject/stats)


cheers
Bruce




On Fri, 3 
Feb 2017, shi yao wang wrote:



Dear Fs experts:I would like to use mris_anatomical_stats to calculate 35 
cortical regions thickness. 
I am using following command: 

mris_anatomical_stats -a subjid/label/lh.aparc.annot -b subjid lh

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[Freesurfer] how to export cortical thickness in to .txt

[shi yao wang]

Dear Fs experts:
I would like to use mris_anatomical_stats to calculate 35 cortical regions
thickness.
I am using following command:

mris_anatomical_stats -a subjid/label/lh.aparc.annot -b subjid lh
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Re: [Freesurfer] how to export cortical thickness in to .txt

[shi yao wang]

Sorry for the interrupted.
My question is how to export the results to .txt files.
I found that there is a -f argument, however it doesnot work.

thanks
Shiyao

On Fri, Feb 3, 2017 at 11:41 AM, shi yao wang 
wrote:

> Dear Fs experts:
> I would like to use mris_anatomical_stats to calculate 35 cortical regions
> thickness.
> I am using following command:
>
> mris_anatomical_stats -a subjid/label/lh.aparc.annot -b subjid lh
>
>
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Re: [Freesurfer] Probability Maps

[Pascal Goodman]

Thanks bruce. Do I upload the entire file? Also,where can I find the link?
Pascal

On Fri, Feb 3, 2017 at 10:35 AM, Bruce Fischl 
wrote:

> Hi Pascal
>
> I don't think tissue priors will help due to the complexity and
> variability of the folding patterns. There may be other interventions
> though - can you send us some examples of where things don't look accurate
> to you?
>
>
> cheers
> Bruce
>
>
> On Fri, 3 Feb 2017, Pascal Goodman wrote:
>
> Hello Bruce, Thanks for replying. I am trying find ways to improve white
>> matter surface (to reduce
>> manual intervention by control points) with the probability map. Also,
>> how do I extract the multiple
>> prior maps you mentioned. Thank you.
>> Best,
>> Pascal
>>
>> On Fri, Feb 3, 2017 at 10:22 AM, Bruce Fischl 
>> wrote:
>>   Hi Pascal
>>
>>   what are you trying to achieve? Internally we have multiple prior
>> maps of this type, but I
>>   don't think we are setup for a user to supply a different one
>>
>>   cheers
>>   Bruce
>>
>>   On Fri, 3 Feb 2017, Pascal Goodman wrote:
>>
>> Hello Freesurfer, I do have a question. Can FS take
>> probability maps of  tissue
>> segmentation as prior?
>> Thanks,
>> Pascal
>>
>>
>>
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Re: [Freesurfer] Probability Maps

[Bruce Fischl]

https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange

tar and gzip an example subject directory and send us the voxel coords of 
points you want us to look at


cheers
Bruce
On Fri, 3 Feb 
2017, Pascal Goodman wrote:



Thanks bruce. Do I upload the entire file? Also,where can I find the link? 
Pascal

On Fri, Feb 3, 2017 at 10:35 AM, Bruce Fischl  
wrote:
  Hi Pascal

  I don't think tissue priors will help due to the complexity and 
variability of the folding
  patterns. There may be other interventions though - can you send us some 
examples of where
  things don't look accurate to you?

  cheers
  Bruce


  On Fri, 3 Feb 2017, Pascal Goodman wrote:

Hello Bruce, Thanks for replying. I am trying find ways to improve 
white matter
surface (to reduce
manual intervention by control points) with the probability map. 
Also, how do I
extract the multiple
prior maps you mentioned. Thank you. 
Best, 
Pascal

On Fri, Feb 3, 2017 at 10:22 AM, Bruce Fischl 

wrote:
      Hi Pascal

      what are you trying to achieve? Internally we have multiple 
prior maps of
this type, but I
      don't think we are setup for a user to supply a different one

      cheers
      Bruce

      On Fri, 3 Feb 2017, Pascal Goodman wrote:

            Hello Freesurfer, I do have a question. Can FS take 
probability maps
of  tissue
            segmentation as prior? 
            Thanks, 
            Pascal



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Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) {Disarmed}

[Erik O'Hanlon]

Thanks for the clarification Eugenio,

Much appreciated

Erik



From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.igles...@ucl.ac.uk]
Sent: 03 February 2017 15:59
To: Freesurfer support list
Subject: Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) {Disarmed}



Hi!
recon-all  -all -3T -s /sub008 -hippocampal-subfields-T1T2 /sub008/sub_008_T2.nii.gz T2Flair
looks good. The flag -hippocampal-subfields-T1FLAIR does not even exist ;-)
Cheers,
/Eugenio






Juan Eugenio Iglesias

ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/








On 3 Feb 2017, at 11:32, Erik O'Hanlon  wrote:

recon-all 
 -all -3T -s /sub008 -hippocampal-subfields-T1T2 /sub008/sub_008_T2.nii.gz T2Flair









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Re: [Freesurfer] Command for Reverse Normalizing with mri_vol2vol Using CVS m3z Morphs (REPOST)

[Douglas Merkitch]

Hey Lilla,

I found the error that I made in the original command I posted; I forgot to 
switch the --targ & --mov inputs in the first mri_vol2vol command. Here's the 
corrected version that works for me:

mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \
--m3z 
$SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \
--noDefM3zPath --inv-morph \
--mov $SUBJECTS_DIR/$subj/mri/norm.mgz \
--o temporary_volume.mgz \
--interp trilin --no-save-reg

mri_vol2vol --targ temporary_volume.mgz \
--reg $SUBJECTS_DIR/$subj/dtrecon/register.dat \
 --inv \
--mov $SUBJECTS_DIR/$subj/dtrecon/lowb.nii \
--o lowb.ANAT+CVS-to-avg35.mgz \
--interp trilin --no-save-reg


Thanks again for the help!

Thanks,

Doug

Douglas Merkitch
Neurological Sciences
Rush University Medical Center






On Jan 31, 2017, at 12:14 PM, Douglas Merkitch 
> wrote:

Hello,

I'm reposting the following just in case anyone has any ideas. Any input would 
be greatly appreciated!

Thank you very much for the suggestion. Here then are my attempts at putting 
what you said into two sequential commands:

mri_vol2vol --targ $SUBJECTS_DIR/$subj/mri/norm.mgz \
--m3z 
$SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \
--noDefM3zPath --inv-morph \
--mov $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \
--o temporary_volume.mgz \
--interp trilin --no-save-reg

mri_vol2vol --targ temporary_volume.mgz \
--reg $SUBJECTS_DIR/$subj/dtrecon/register.dat \
--inv \
--mov $SUBJECTS_DIR/$subj/dtrecon/lowb.nii \
--o lowb.ANAT+CVS-to-avg35.mgz \
--interp trilin --no-save-reg

Do the above commands look OK? I tried these commands, but the results were not 
great so I suspect that something is incorrect in the syntax and/or inputs.

Thanks,

Doug

Douglas Merkitch
Neurological Sciences
Rush University Medical Center



On Jan 26, 2017, at 2:41 PM, Douglas Merkitch 
> wrote:

Hello Lilla,

Thank you very much for the suggestion. Here then are my attempts at putting 
what you said into two sequential commands:

mri_vol2vol --targ $SUBJECTS_DIR/$subj/mri/norm.mgz \
--m3z 
$SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \
--noDefM3zPath --inv-morph \
--mov $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \
--o temporary_volume.mgz \
--interp trilin --no-save-reg

mri_vol2vol --targ temporary_volume.mgz \
--reg $SUBJECTS_DIR/$subj/dtrecon/register.dat \
--inv \
--mov $SUBJECTS_DIR/$subj/dtrecon/lowb.nii \
--o lowb.ANAT+CVS-to-avg35.mgz \
--interp trilin --no-save-reg

Do the above commands look OK? I tried these commands, but the results were not 
great so I suspect that something is incorrect in the syntax and/or inputs.

Thanks for your help!

Doug

Douglas Merkitch
Neurological Sciences
Rush University Medical Center
Email: douglas_merki...@rush.edu





On Jan 26, 2017, at 8:42 AM, Lilla Zollei 
>
 wrote:


Hi Doug,

In order to compute and apply the inverse of an m3z transform you would need to 
use the --inv-morph flag instead of the --m3z and reverse your targ and mov 
inputs. With the current implementation of mri_vol2vol though I do not think 
that you can specify the order of the transforms (which is important here), so 
you would need to apply the inverse non-linear trasform first and then the 
inverse rigid.

Lilla

On Wed, 25 Jan 2017, Douglas Merkitch wrote:

Hello Freesurfer experts,
>From your wiki page, I understand how to normalize volumes in subject 
>diffusion space to the CVS template:
mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \
   --m3z 
$SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \
   --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \
   --mov fa-masked.mgz \
   --o fa-masked.ANAT+CVS-to-avg35.mgz \
   --interp trilin --no-save-reg
However, how would one take take a volume in CVS template space and reverse 
normalize it back to subject diffusion space? Is this possible? If so, what 
would that command look like and what other st
eps would be necessary to get the required inputs?
Thanks,
Doug
Douglas Merkitch
Neurological Sciences
Rush University Medical Center
Email: douglas_merki...@rush.edu
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Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) {Disarmed}

[Iglesias Gonzalez, Eugenio]

Hi!
recon-all  -all -3T -s /sub008 -hippocampal-subfields-T1T2 
/sub008/sub_008_T2.nii.gz T2Flair
looks good. The flag -hippocampal-subfields-T1FLAIR does not even exist ;-)
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 3 Feb 2017, at 11:32, Erik O'Hanlon 
> wrote:

recon-all  -all -3T -s /sub008 -hippocampal-subfields-T1T2 
/sub008/sub_008_T2.nii.gz T2Flair

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Re: [Freesurfer] Probability Maps

[Bruce Fischl]

Hi Pascal

I don't think tissue priors will help due to the complexity and 
variability of the folding patterns. There may be other interventions 
though - can you send us some examples of where things don't look accurate 
to you?


cheers
Bruce


On Fri, 3 Feb 2017, Pascal Goodman 
wrote:



Hello Bruce, Thanks for replying. I am trying find ways to improve white matter 
surface (to reduce
manual intervention by control points) with the probability map. Also, how do I 
extract the multiple
prior maps you mentioned. Thank you. 
Best, 
Pascal

On Fri, Feb 3, 2017 at 10:22 AM, Bruce Fischl  
wrote:
  Hi Pascal

  what are you trying to achieve? Internally we have multiple prior maps of 
this type, but I
  don't think we are setup for a user to supply a different one

  cheers
  Bruce

  On Fri, 3 Feb 2017, Pascal Goodman wrote:

Hello Freesurfer, I do have a question. Can FS take probability 
maps of  tissue
segmentation as prior? 
Thanks, 
Pascal



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Re: [Freesurfer] Probability Maps

[Pascal Goodman]

Hello Bruce,
Thanks for replying. I am trying find ways to improve white matter surface
(to reduce manual intervention by control points) with the probability map.
Also, how do I extract the multiple prior maps you mentioned. Thank you.
Best,
Pascal

On Fri, Feb 3, 2017 at 10:22 AM, Bruce Fischl 
wrote:

> Hi Pascal
>
> what are you trying to achieve? Internally we have multiple prior maps of
> this type, but I don't think we are setup for a user to supply a different
> one
>
> cheers
> Bruce
>
>
> On Fri, 3 Feb 2017, Pascal Goodman wrote:
>
> Hello Freesurfer, I do have a question. Can FS take probability maps of
>>  tissue segmentation as prior?
>> Thanks,
>> Pascal
>>
>>
>>
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Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) {Disarmed}

[Erik O'Hanlon]

Thanks Bruce,

Much appreciated

Best regards

Erik

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: 03 February 2017 15:18
To: Freesurfer support list
Subject: Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags 
(freesurfer v6) {Disarmed}

Hi Erik

Eugenio can confirm, but I don't think the subfield stuff cares. The
-hippocampal-subfields-T1T2 means use multiple inputs, but it doesn't
assume anything about the distribution of intensities in them.

cheers
Bruce
On Fri, 3 Feb
2017, Erik O'Hanlon wrote:

> Hi Experts,
>
> Just flowing on from Joe's question, I have run my analysis without the T2 or 
> FLAIR flag but have
> specificed the T2 which is a FLAIR image for the hippocampal subfield 
> options. I have used
>
> recon-all  -all -3T -s /sub008 -hippocampal-subfields-T1T2 
> /sub008/sub_008_T2.nii.gz T2Flair
>
> Should I have used -hippocampal-subfields-T1FLAIR instead? Can I change this 
> and simply rerun without
> the need to do everything from scratch.
> I have T2 and FLAIR images that I havent used for pial correction, can I add 
> that in too and if so which
> is best teh T2 or the FLAIR or both?
>
> Thanks and as always, really appreciate the help
>
> Cheers
>
> Erik
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Joe
> Necus (PGR) [j.nec...@newcastle.ac.uk]
> Sent: 03 February 2017 10:56
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags 
> (freesurfer v6) {Disarmed}
>
> Thanks for the quick reply. I'll re-run my subjects with the -FLAIR flag.
>
>
> Joe
>
>
>
> Erik O'Hanlon
> Postdoctoral researcher
>
> [IMAGE]
>
> RCSI Psychiatry
> Royal College of Surgeons in Ireland
> Beaumont Road, Beaumont, D9, Ireland
> T: 8093740
> E: erikohan...@rcsi.ie W: www.rcsi.ie
>
> RCSI DEVELOPING HEALTHCARE LEADERS
> WHO MAKE A DIFFERENCE WORLDWIDE
>
>
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Bruce
> Fischl 
> Sent: 02 February 2017 22:56
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags 
> (freesurfer v6)
> Hi Joe
>
> there are slight differences, and for sure we reserve the right to use
> the knowledge that it is a FLAIR scan in the algorithms, so you should
> probably rerun
>
> cheers
> Bruce
> On Thu, 2 Feb 2017, Joe Necus (PGR) wrote:
>
> >
> > Hello,
> >
> >
> > I am running recon-all on the latest version of freesurfer (Version 6) and 
> > would like to know whether
> > there is any difference between using the -T2 -T2Pial and -Flair flags.
> >
> >
> > I am currently running recon-all with a T1 and FLAIR image, but have used 
> > the -T2 -T2pial flags and
> > would like to know whether I need to go back and instead re-run with the 
> > -FLAIR flag instead.
> >
> >
> > Thanks a lot,
> >
> > Joe
> >
> >
> >
> >
> >
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Re: [Freesurfer] Probability Maps

[Bruce Fischl]

Hi Pascal

what are you trying to achieve? Internally we have multiple prior maps of 
this type, but I don't think we are setup for a user to supply a different 
one


cheers
Bruce

On Fri, 3 Feb 2017, Pascal Goodman wrote:


Hello Freesurfer, I do have a question. Can FS take probability maps of  tissue 
segmentation as prior? 
Thanks, 
Pascal


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Re: [Freesurfer] possible atlas error to report

[Bruce Fischl]

Hi Jacob

the unthresholded BA44 spreads over a lot of prefrontal cortex as low 
probability but possible locations for 44. Using it confounds variability 
with size.


cheers
Bruce


On Fri, 3 Feb 2017, Levman, Jacob wrote:


The following pair are consistent:
lh.BA.thresh BA44 GrayVol
rh.BA.thresh BA44 GrayVol

The following pair are inconsistent:
lh.BA BA44 GrayVol
rh.BA BA44 GrayVol
Other measurements in the lh.BA and rh.BA atlases may also be inconsistent.

Thanks,

Jacob

From: freesurfer-boun...@nmr.mgh.harvard.edu  
on behalf of Douglas N Greve 
Sent: 02 February 2017 16:40
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] possible atlas error to report

Sorry, which labels are consistent and which are inconsistent?


On 02/02/2017 02:52 PM, Levman, Jacob wrote:


Hi there,


I've been conducting an asymmetry analysis based on FreeSurfer
measurements. There are regions of the brain with known left-right
asymmetry such as BA44 which exhibits strong leftward asymmetry (the
left side is bigger than the right). This is accurately reflected when
you compare the BA44 GrayVol measurement from lh.BA.thresh to
rh.BA.thresh. However, in the lh.BA and rh.BA results, the BA44
GrayVol measurements consistently indicate a rightward asymmetry
(right side larger than the left side) though this conflicts with
known findings in the literature for this region of the brain and is
the opposite pattern to that produced in lh.BA.thresh and rh.BA.thresh.


This indicates that the lh.BA and rh.BA results may be left-right
inverted in BA44 and possibly in other regions as well.


Thanks,


Jacob


​




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Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) {Disarmed}

[Bruce Fischl]

Hi Erik

Eugenio can confirm, but I don't think the subfield stuff cares. The 
-hippocampal-subfields-T1T2 means use multiple inputs, but it doesn't 
assume anything about the distribution of intensities in them.


cheers
Bruce
On Fri, 3 Feb 
2017, Erik O'Hanlon wrote:



Hi Experts,

Just flowing on from Joe's question, I have run my analysis without the T2 or 
FLAIR flag but have
specificed the T2 which is a FLAIR image for the hippocampal subfield options. 
I have used

recon-all  -all -3T -s /sub008 -hippocampal-subfields-T1T2 
/sub008/sub_008_T2.nii.gz T2Flair

Should I have used -hippocampal-subfields-T1FLAIR instead? Can I change this 
and simply rerun without
the need to do everything from scratch.
I have T2 and FLAIR images that I havent used for pial correction, can I add 
that in too and if so which
is best teh T2 or the FLAIR or both?

Thanks and as always, really appreciate the help

Cheers

Erik


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Joe
Necus (PGR) [j.nec...@newcastle.ac.uk]
Sent: 03 February 2017 10:56
To: Freesurfer support list
Subject: Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags 
(freesurfer v6) {Disarmed}

Thanks for the quick reply. I'll re-run my subjects with the -FLAIR flag.


Joe



Erik O'Hanlon
Postdoctoral researcher

[IMAGE]

RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740
E: erikohan...@rcsi.ie W: www.rcsi.ie

RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE  

 


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce
Fischl 
Sent: 02 February 2017 22:56
To: Freesurfer support list
Subject: Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags 
(freesurfer v6)  
Hi Joe

there are slight differences, and for sure we reserve the right to use
the knowledge that it is a FLAIR scan in the algorithms, so you should
probably rerun

cheers
Bruce
On Thu, 2 Feb 2017, Joe Necus (PGR) wrote:

>
> Hello,
>
>
> I am running recon-all on the latest version of freesurfer (Version 6) and 
would like to know whether
> there is any difference between using the -T2 -T2Pial and -Flair flags.
>
>
> I am currently running recon-all with a T1 and FLAIR image, but have used the 
-T2 -T2pial flags and
> would like to know whether I need to go back and instead re-run with the 
-FLAIR flag instead.
>
>
> Thanks a lot,
>
> Joe
>
>
>
>
>
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Re: [Freesurfer] Specification of computer

[Bruce Fischl]

Hi Aziz

with multiple course you can specify -openmp 8 for exmaple to use 8 cores, 
which speeds things up a lot. It also depends how many recons you will be 
running at the same time. A 16 core machine with 64G of ram would be able 
to run 4 recons in a few hours each.


cheers
Bruce

On Fri, 3 Feb 2017, Aziz 
Nanthaamornphong wrote:



Hi experts,
I would like to find a new high-performance computer to run the reconstruction 
process in Freesurfer. 
Currently, I used a single computer (Intel core i7, RAM 8MB) to run the 
commands (e.g., 'recon-all -all'
) that spent average time 7-9 hours per one subject data. 

Please let me know what the best spec of the computer that can reduce the time 
to 2-3 hours (if
possible). 

Thank you,
Aziz

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[Freesurfer] [FSFAST] Matlab parallel

[Seung-Goo KIM]

Hi all,

So this is a question about running FAST through matlab parallel desktop: I 
know it is very funny (and inefficient) because I open up a bash in the matlab 
to run a csh script that generates and runs a matlab code, but just I’m 
familiar with matlab in doing many things including string manipulation, so 
that’s how I’m doing now. If there are matlab scripts that does a similar thing 
as csh scripts, it would be nice.

Anyway, I realized that I cannot run all the fitting with different parameters 
and with the identical name of model (the GLM directory name) at the same time 
because the code appears to refer to the directory at $SUBJECTS_DIR. 

But I tried to run multiple subjects (with all different GLM names in their own 
native spaces) through MATLAB on a server, it returns (seems just one of random 
subject):

> ERROR: could not read /tmp/tmp354512.nii
> rm: cannot remove ‘/tmp/tmp354512.nii’: No such file or directory
> ERROR: loading ${filename}.nii.gz as analyze

So I traced back to the functions that return those errors (i.e., load_nifti.m 
run in MRIread.m) and it seems to be something with the temporary directory 
managed by matlab workers. The temporary file seems to be only necessary for 
nii.gz file. 

If so, I would rather just use .nii file format (or maybe .mgz?) format instead 
of dealing with the void complexity. Then can it be done by just putting:

> setenv(‘FSF_OUTPUTFORMAT’,’.mgz’) 


before I run "preproc-sess" and "selxavg3-sess” in my scripts?

Best regards,
-- 
Seung-Goo KIM

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[Freesurfer] Contrast percent map

[Seung-Goo KIM]

Hi Doug,

Thank you so much for clarification. Probably there is an issue with the 
mailing list, I only received the digest list, and now I saw your reply.

In fact, I found it by myself while looking through fast_selxavg3.m: the 
baseline being defined by the overall offset. and yes, I was thinking something 
else.. because contrast=(baseline+contrast)-baseline, so it’s just 
contrast/offset*100

Thanks!
-SG

> From: Douglas Greve  >
> Subject: Re: [Freesurfer] [FSFAST] Contrast percent map
> Date: 1 February 2017 at 17:38:35 GMT+1
> To: freesurfer@nmr.mgh.harvard.edu 
> 
> 
> you have the right idea, but it is
> 
> cespct = 100*contrast/baseline
> 
> The baseline is the mean offset of the fMRI, the contrast is the deviation 
> from baseline
> 
> 
> On 2/1/17 4:49 AM, Seung-Goo KIM wrote:
>> Dear all,
>> 
>> I wish to know how “cespct.nii.gz” is computed in selxavg3-sess. I thought 
>> it computes something like a relative change like: 
>> 
>> cespct = (contrast-baseline)/baseline*100, 
>> 
>> but I cannot figure out what was taken for the baseline. I thought it could 
>> be mean beta for constant terms (0-th polynomial) for each run, but my 
>> calculation was different from cespct.
>> 
>> I would take average intensity for each voxel I would greatly appreciate a 
>> detailed explanation how the program computes it.
>> 
>> Best regards,
>> -- 
>> Seung-Goo KIM
-- 
Seung-Goo KIM

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[Freesurfer] Probability Maps

[Pascal Goodman]

Hello Freesurfer,
I do have a question. Can FS take probability maps of  tissue segmentation
as prior?
Thanks,
Pascal
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Re: [Freesurfer] possible atlas error to report

[Levman, Jacob]

The following pair are consistent:
lh.BA.thresh BA44 GrayVol
rh.BA.thresh BA44 GrayVol

The following pair are inconsistent:
lh.BA BA44 GrayVol
rh.BA BA44 GrayVol
Other measurements in the lh.BA and rh.BA atlases may also be inconsistent.

Thanks,

Jacob

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

Sent: 02 February 2017 16:40
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] possible atlas error to report

Sorry, which labels are consistent and which are inconsistent?


On 02/02/2017 02:52 PM, Levman, Jacob wrote:
>
> Hi there,
>
>
> I've been conducting an asymmetry analysis based on FreeSurfer
> measurements. There are regions of the brain with known left-right
> asymmetry such as BA44 which exhibits strong leftward asymmetry (the
> left side is bigger than the right). This is accurately reflected when
> you compare the BA44 GrayVol measurement from lh.BA.thresh to
> rh.BA.thresh. However, in the lh.BA and rh.BA results, the BA44
> GrayVol measurements consistently indicate a rightward asymmetry
> (right side larger than the left side) though this conflicts with
> known findings in the literature for this region of the brain and is
> the opposite pattern to that produced in lh.BA.thresh and rh.BA.thresh.
>
>
> This indicates that the lh.BA and rh.BA results may be left-right
> inverted in BA44 and possibly in other regions as well.
>
>
> Thanks,
>
>
> Jacob
>
>
> ​
>
>
>
>
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Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) {Disarmed}

[Erik O'Hanlon]

Hi Experts,

Just flowing on from Joe's question, I have run my analysis without the T2 or FLAIR flag but have specificed the T2 which is a FLAIR image for the hippocampal subfield options. I have used

recon-all  -all -3T -s /sub008 -hippocampal-subfields-T1T2 /sub008/sub_008_T2.nii.gz T2Flair

Should I have used -hippocampal-subfields-T1FLAIR instead? Can I change this and simply rerun without the need to do everything from scratch.
I have T2 and FLAIR images that I havent used for pial correction, can I add that in too and if so which is best teh T2 or the FLAIR or both?

Thanks and as always, really appreciate the help

Cheers

Erik 


From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Joe Necus (PGR) [j.nec...@newcastle.ac.uk]
Sent: 03 February 2017 10:56
To: Freesurfer support list
Subject: Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) {Disarmed}





Thanks for the quick reply. I'll re-run my subjects with the -FLAIR flag.


Joe





Erik O'Hanlon 

Postdoctoral researcher



RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740

E: erikohan...@rcsi.ie W: www.rcsi.ie

RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE  

 

From: freesurfer-boun...@nmr.mgh.harvard.edu  on behalf of Bruce Fischl 
Sent: 02 February 2017 22:56
To: Freesurfer support list
Subject: Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6)
 



Hi Joe

there are slight differences, and for sure we reserve the right to use 
the knowledge that it is a FLAIR scan in the algorithms, so you should 
probably rerun

cheers
Bruce
On Thu, 2 Feb 2017, Joe Necus (PGR) wrote:

> 
> Hello,
> 
> 
> I am running recon-all on the latest version of freesurfer (Version 6) and would like to know whether
> there is any difference between using the -T2 -T2Pial and -Flair flags.
> 
> 
> I am currently running recon-all with a T1 and FLAIR image, but have used the -T2 -T2pial flags and
> would like to know whether I need to go back and instead re-run with the -FLAIR flag instead.
> 
> 
> Thanks a lot,
> 
> Joe
> 
> 
> 
> 
>
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[Freesurfer] Specification of computer

[Aziz Nanthaamornphong]

Hi experts,

I would like to find a new high-performance computer to run the
reconstruction process in Freesurfer.  Currently, I used a single computer
(Intel core i7, RAM 8MB) to run the commands (e.g., 'recon-all -all' ) that
spent average time 7-9 hours per one subject data.

Please let me know what the best spec of the computer that can reduce the
time to 2-3 hours (if possible).

Thank you,
Aziz
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Re: [Freesurfer] extract values uncorrected clusters

[Clara Kühn]

Hi Doug,

thanks for your reply. I'm trying it out but I get this error message: 
ERROR: srcsubjid must be supplied

I have 40 subjects in 2 groups. What exactly do I enter as --subject ?

Thanks for your help!
Clara


- Ursprüngliche Mail -
Von: "Douglas N Greve" 
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Mittwoch, 1. Februar 2017 19:18:55
Betreff: Re: [Freesurfer] extract values uncorrected clusters

You can run mri_surfcluster using the sig.mgh as the input and 
specifying a --minarea and --thmin .001. --minarea takes a surface area 
in mm2, not number of vertices, so you'll have to compute what the 
approx area is of 150 vertices. Include a --ocn output and --sum 
sumfile, then use mri_segstats with --seg ocn.mgh --excludeid 0 --i 
y.mgh --avgwf y.sum.dat

The output y.sum.dat will be a matrix of number of subjects by number of 
clusters. Look in the sumfile for the cluster identity


On 02/01/2017 11:41 AM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> I did a group analysis in QDEC for the symmetric percent change from pre to 
> post and have a couple of clusters that don't survive the Monte Carlo 
> correction. I want to extract the values for each time point per subject for 
> those clusters that are bigger than 150 vertices to look at individual 
> trends. How could I achieve this?
>
> Thank you for your help.
> Clara
>
>
> -
> Clara Kühn, Phd Student
>   
> Max-Planck-Institute for Human Cognitive and Brain Science
> Department of Neuropsychology
> Stephanstrasse 1A
> 04103 Leipzig, Germany
>
> Phone: +49 341 - 9940 2271
> Fax: +49 341 - 9940 2260
> Web: www.cbs.mpg.de
> E-Mail: cku...@cbs.mpg.de
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) {Disarmed}

[Joe Necus (PGR)]

Thanks for the quick reply. I'll re-run my subjects with the -FLAIR flag.


Joe



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: 02 February 2017 22:56
To: Freesurfer support list
Subject: Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags 
(freesurfer v6)

Hi Joe

there are slight differences, and for sure we reserve the right to use
the knowledge that it is a FLAIR scan in the algorithms, so you should
probably rerun

cheers
Bruce
On Thu, 2 Feb 2017, Joe Necus (PGR) wrote:

>
> Hello,
>
>
> I am running recon-all on the latest version of freesurfer (Version 6) and 
> would like to know whether
> there is any difference between using the -T2 -T2Pial and -Flair flags.
>
>
> I am currently running recon-all with a T1 and FLAIR image, but have used the 
> -T2 -T2pial flags and
> would like to know whether I need to go back and instead re-run with the 
> -FLAIR flag instead.
>
>
> Thanks a lot,
>
> Joe
>
>
>
>
>
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University
mail.nmr.mgh.harvard.edu
To see the collection of prior postings to the list, visit the Freesurfer 
Archives. A searchable archive which of messages PRIOR to March 2004 is at ...





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contains patient information, please contact the Partners Compliance HelpLine at
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mycompliancereport.com
www.partners.org
ComplianceLine engages in the business of providing 24-hour toll-free hotlines 
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identification of possible unethical, illegal or questionable behavior.



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Re: [Freesurfer] How to check recon-all finished without any error

[Sebastian Huhn]

Dear Emroy,

I can also recommend using QA tools:
https://surfer.nmr.mgh.harvard.edu/fswiki/QATools

You can edit the "default_status_log_xx" files in the folder and enter the 
steps that you're interested in.

Give it a try.
Kind regards,

Sebastian

- Original Message -
From: "Trisanna Sprung-Much" 
To: "Freesurfer support list" 
Sent: Thursday, February 2, 2017 9:43:32 PM
Subject: Re: [Freesurfer] How to check recon-all finished without any error

Try checking your recon all.log in your scripts folder of the subject. 

Trisanna 

-- 
Ph.D. Candidate 
McGill University 
Integrated Program in Neuroscience 
Psychology 


On Thu, Feb 2, 2017 at 1:52 PM, shi yao wang < wangshiyao2...@gmail.com > 
wrote: 



Dear FS experts: 
How to check recon-all finished without any error? 
Sometime, there are showing no error message, however, when I running 
hippocampus subfield, it does not run. 

thanks 
Lawrence 
Emory 

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[Freesurfer] Regarding: mris_label2annot

[Dr Sampada Sinha]

Dear freesurfer experts,

I am trying to create medial temporal lobe and for that I ran the command
mri_annotation2label to create ?h.entorhinal.label, ?h.temporalpole.label
and ?h.parahippocampal.label from fsaverage and stored these labels in
labels.?h directory. After this I ran mris_label2annot, taking cue from
page https://surfer.nmr.mgh.harvard.edu/fswiki/mris_label2annot.

My command line is the following (fsaverage has been linked to my subject
directory:

rmbp:AD Sampada$ mris_label2annot  --s fsaverage --h lh --ctab
/Applications/freesurfer/subjects/bert/label/aparc.annot.ctab --a myaparc
--l ./labels_lh/lh.temporalpole.label --l
./labels_lh/lh.parahippocampal.label --l ./labels_lh/lh.entorhinal.label
--nhits nhits.mgh

However, it comes with following error

*Writing annot to
/Users/Sampada/Desktop/AD/fsaverage/label/lh.myaparc.annot*
*could not write annot file
/Users/Sampada/Desktop/AD/fsaverage/label/lh.myaparc.annot*
*Permission denied*

Will you please let me know how to fix this problem . I can see its
a permission error but don't know how to overcome it.

Thanks for your help

Kind regards,

Sampada

-- 
Sampada
​Research medical scientist (B)​
Department of Geriatric Mental Health (DGMH)
King George Medical University
Lucknow-226003
​, Uttar Pradesh​
India
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[Freesurfer] Fw: Analysis of rates or percent changes

[Katarina Trojacanec]

Hi Martin,


Apologies for multiple e-mails, but I got a message that something might be 
wrong with the previous e-mail, so I forward it again.


Please find below my previous question.


Regards, Katarina


Katarina Trojacanec, M.Sc.
Teaching and research assistant

Faculty of Computer Science and Engineering
Ss. Cyril and Methodius University - Skopje, Republic of Macedonia


From: Katarina Trojacanec
Sent: Thursday, February 2, 2017 2:46 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Analysis of rates or percent changes


Hi Martin,


I dropped --generic-time flag as you suggested in the previous e-mail and run 
the long_stats_slopes command again like this:


long_stats_slopes --qdec ./qdec/long_AD_NL_TP1_2_3_4.qdec.table.dat --stats 
aseg.stats --meas volume --sd $SUBJECTS_DIR --do-rate --do-pc1fit --do-pc1 
--do-spc --time years --stack-rate 
./qdec/long_AD_NL_TP1_2_3_4_m.aseg-rate.stack.txt --stack-pc1fit 
./qdec/long_AD_NL_TP1_2_3_4_m.aseg-pc1fit.stack.txt --stack-pc1 
./qdec/long_AD_NL_TP1_2_3_4_m.aseg-pc1.stack.txt --stack-spc 
./qdec/long_AD_NL_TP1_2_3_4_m.aseg-spc.stack.txt

However, I got exactly the same results for stacked rate pc1/fit, spc (the 
files long_AD_NL_TP1_2_3_4_m.aseg-*.stack.txt) as in the case with the 
--generic-time flag. Is this reasonable?


As I read and understood, the --generic-time flag assumes that time difference 
between the time points is 1, which is not true in my case (the time difference 
between TP1 and TP2 is around six months, and between TP2 and TP3, as well as 
TP3 and TP4 is one year). This indicates that there should be some difference 
in the result.


Am I doing something wrong or misunderstood anything, or maybe there are some 
temporary files from the first running of the command that are used also in the 
second one (without --generic-time flag)?


Best, Katarina


Katarina Trojacanec, M.Sc.
Teaching and research assistant

Faculty of Computer Science and Engineering
Ss. Cyril and Methodius University - Skopje, Republic of Macedonia


From: Katarina Trojacanec
Sent: Monday, September 12, 2016 10:01:53 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Analysis of rates or percent changes


Hi Martin,


Thanks a lot.


Best, Katarina


Katarina Trojacanec, M.Sc.
Teaching and research assistant

Faculty of Computer Science and Engineering
Ss. Cyril and Methodius University - Skopje, Republic of Macedonia


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Martin Reuter 

Sent: Monday, September 12, 2016 7:58:14 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Analysis of rates or percent changes


Hi Katarina,


different time spacing is OK (not optimal, but OK). This 2-stage procedure 
first fits a line in each subject, independent on how many time points the 
subject has. Of course a linear fit from 4 time points will be more reliable 
than one from just 2 time points. This is not taken into consideration and 
therefore we usually recommend the Linear Mixed Effects modeling (where it is 
considered in the model). If most of your subjects have 4 time points and the 
spacing is similar (across subjects) you should be fine.


Other things I noticed:

- you should drop the --generic-time flag. I probably should change the help 
text to be more specific, but what it does it assigns a time of 1 2 3 4 to the 
time points (this is if you do repeated measures and there is no real time). So 
don't pass it.


- you can drop some of the --do... flags. Probably you are interested in the 
rate and one of the pct change flags. The average is just the average thickness 
(across time) for each subject. Not sure you want to analyze that. The 
--do-stack is a subject-specific stack of the time points, usually only used 
for debugging.


- the -stack-avg is not needed unless you want to analyze average thickness for 
each subject, rather you may want to create a stack for the rate or the pc1 or 
whatever, to pass it into the stats tool (like mri_glmfit, or R, SPSS or 
whatever you use).


Best, Martin


On 09/12/2016 12:40 PM, Katarina Trojacanec wrote:

Hi,


I have a question about the analysis of rates or percent changes.


I use data with available scans at baseline (TP1) and the 6-month (TP2), 
12-month (TP3) and 24-month (TP4) follow-ups from ADNI dataset. An example of 
some of the data in the appropriate qdec table is given below:


fsid fsid-base years age weight diagnosis gender Glob_CDR NPI-Q_TotScr 
MMSE_TotScr FAQ_TotScr visit1_2_3_4
ADNI_sub1_sc ADNI_base1 0 81.3 y AD M x x x x sc
ADNI_sub1_m06 ADNI_base1 0.528767123 81.9 y AD M x x x x m06
ADNI_sub1_m12 ADNI_base1 1.030136986 82.4 y AD M x x x x m12
ADNI_sub1_m24 ADNI_base1 2.030136986 83.4 y AD M x x x x m24
ADNI_sub2_sc ADNI_base2 0 74 y AD F x x x x sc
ADNI_sub2_m06 ADNI_base2 0.501369863 74.5 y AD