Re: [Freesurfer] recon-all -hires option

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

If you want to try to do it systematically, you can add -wsless (should reduce 
the agressiveness of the skull strip)

On 1/4/2021 3:52 AM, 
falk.luesebr...@med.ovgu.de wrote:

External Email - Use Caution

Hi Simon,


in case your surfaces (and other outputs) look fine, there is no need to worry 
about the skull stripping too much. However, in case you what to do something 
about this you can do either of the following.


Which version are you using? I assume v6? In v7 the hires option basically has 
changed to what was known as the HCP pipeline before. Here, only the surface 
related parts of FreeSurfer are handled in native space. The other stages are 
handled in resampled 1mm space. Therefore, you will benefit from your higher 
resolution, while not having any of these issues. There are also some other 
stages included which may help with high resolution 3T data (e.g. denoising 
prior to surface placement).


In case you want to stick with v6 and what to run everything in native space, 
you can get better skull stripping following the first few steps from this 
guide I put together few years ago (and is still valid today):

https://secure-web.cisco.com/1cP9GZTFwQIDCR-WcWJPQA-tzd6FKvDGnFtvVRx4GcsgT8p3OTg1qClc-Hq--pwQhCCzMU0__8jGrDJugvajjUrRsHuOiOAOaxFIABpq99gkP60a9dQB2KDoTXXK3jmPU66oLOS0VCPGhxL5_1DVsdUVWefugGXKw6nA29BxCzBaKOfrZBOuL4bxxOBVIVUa1E3EfYzL7gMPd6g5Xvqz1zUtRdv-sQtDWX98QT7ZaoRAjjeDZvgWcqjhe9WNHXE5kInE_ok7pb2gunRxE78zPKg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHiResRecon


What you basically do is to run the 1mm stream to create a nice brainmask (or 
any other tool you like), resample that to the resolution of your high 
resolution stream and apply the mask after the normalization stage. Then 
continue with autorecon2 and autrecon3.


Best,

Falk



Von: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 im Auftrag von S.R. Poortman 

Gesendet: Montag, 4. Januar 2021 09:13:11
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Fw: recon-all -hires option


External Email - Use Caution

Dear list members,

As a PhD student working on longitudinal child and adolescent T1-weighted data 
(.75x.75x.8 mm3) acquired at 3T (age range: 8 - 18 at baseline; 11 - 24 at 
follow-up), with the aim of doing cortical laminar analyses eventually, I am 
interested in getting the most of our lab's submillimeter resolution data. 
Therefore, in addition to a default recon-all run (with the -3T option 
enabled), I ran a separate recon-all with both the -3T and the -hires option 
enabled (with mris_inflate -n 50 added to the expert file), resulting in the 
following two runs:
recon-all -all -i ${subj} -subjid ${SUB_ID} -3T
and
recon-all -all -i ${subj} -subjid ${SUB_ID}  -3T -hires -expert $EXPERT_FILE
Now, the surfaces (i.e., lh.pial, lh.white, rh.pial, rh.white) seem to be 
calculated more accurately for most brain regions, indeed, which looks very 
promising. However, the brainmask.mgz turns out to be of poor quality for a 
number of our subjects, cutting away a substantial portion of the brain. See 
the image below for an example of the same subject, on which both runs have 
been performed. The same slices are shown for each run. As can be seen in the 
image, a part of the the temporal region of the brain has been excluded in the 
brainmask.mgz of the -hires run (left in the image).

[cid:b4d26f40-11bb-4d8f-888c-ab4da9fea062]

Is there anything I can do, such as adjusting certain parameters, to prevent 
this from occurring? It would be a shame if I couldn't make use of the -hires 
option due to this, as it does seem to be a promising option in all other 
aspects.

Thank you for considering my question. I look forward to hearing from you.

Good holidays to you!

Kind regards,
Simon Poortman (Erasmus MC, Rotterdam, the Netherlands)





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Re: [Freesurfer] recon-all -hires

[Nasiriavanaki, Zahra]

Hi Doug


Thank you very much for your reply.

Actually the recon finished today without any error. It just took so long to be 
done for only one subject (almost two days!)!

I checked the registration and It looks ok.

I will try -conf2hires for my other subject that -hires didn't work on it.


Thanks

Mona


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

Sent: Friday, February 22, 2019 1:07:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all -hires

sometimes the -hires flag does not work very well. For the subjects where it 
does complete, do the surfaces look ok? You can also use recon-all.v6.hires 
with the -conf2hires option (available in fs6 on our network).

On 2/21/19 2:36 PM, Nasiriavanaki, Zahra wrote:

Hi Bruce


Thank you very much for  your reply.

Here is my command:

recon-all -all -s ${subj} -i  ./${subj}/anat/016/mT1v2.nii -expert  
./scripts/expertopts/expert.opts -hires -mail zn025 -parallel

I also attached my .log file.


Thanks

MOna



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Bruce Fischl 
<mailto:fis...@nmr.mgh.harvard.edu>
Sent: Thursday, February 21, 2019 2:23:14 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all -hires

Hi MOna


what was your full command line? And can you send us the recon-all.log
file?

cheers
Bruce
On Thu, 21 Feb 2019, Nasiriavanaki, Zahra wrote:

>
> Dear Freesurfer experts
>
>
> I was running recon-all command with hires flag for our high resolution fMRI 
> data, but it has been in a
> constant status since yesterday.
>
> I copied the last few lines that are currently in my terminal. I had the same 
> issue with another
> subject before, and I had to terminate the recon-all and run it without 
> -hires.
>
> Could you please let me know how I can solve this issue?
>
>
> Thanks
>
> Mona
>
>
>
> #@# Fix Topology Copy rh Wed Feb 20 19:50:00 EST 2019
> /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/scripts
>
>  cp ../surf/rh.orig.nofix ../surf/rh.orig
>
>
>  cp ../surf/rh.inflated.nofix ../surf/rh.inflated
>
> #@# Fix Topology lh Wed Feb 20 19:50:03 EST 2019
>
>  mris_fix_topology 
> -rusage/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/touch/rusage.mris_fix_topology.
> lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 inul_loom2_7T lh
>
> #@# Fix Topology rh Wed Feb 20 19:50:03 EST 2019
>
>  mris_fix_topology 
> -rusage/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/touch/rusage.mris_fix_topology.
> rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 inul_loom2_7T rh
>
> Waiting for PID 8994 of (8994 8997) to complete...
>
>
>
>
>



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Re: [Freesurfer] recon-all -hires

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

sometimes the -hires flag does not work very well. For the subjects where it 
does complete, do the surfaces look ok? You can also use recon-all.v6.hires 
with the -conf2hires option (available in fs6 on our network).

On 2/21/19 2:36 PM, Nasiriavanaki, Zahra wrote:

Hi Bruce


Thank you very much for  your reply.

Here is my command:

recon-all -all -s ${subj} -i  ./${subj}/anat/016/mT1v2.nii -expert  
./scripts/expertopts/expert.opts -hires -mail zn025 -parallel

I also attached my .log file.


Thanks

MOna



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Bruce Fischl 
<mailto:fis...@nmr.mgh.harvard.edu>
Sent: Thursday, February 21, 2019 2:23:14 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all -hires

Hi MOna


what was your full command line? And can you send us the recon-all.log
file?

cheers
Bruce
On Thu, 21 Feb 2019, Nasiriavanaki, Zahra wrote:

>
> Dear Freesurfer experts
>
>
> I was running recon-all command with hires flag for our high resolution fMRI 
> data, but it has been in a
> constant status since yesterday.
>
> I copied the last few lines that are currently in my terminal. I had the same 
> issue with another
> subject before, and I had to terminate the recon-all and run it without 
> -hires.
>
> Could you please let me know how I can solve this issue?
>
>
> Thanks
>
> Mona
>
>
>
> #@# Fix Topology Copy rh Wed Feb 20 19:50:00 EST 2019
> /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/scripts
>
>  cp ../surf/rh.orig.nofix ../surf/rh.orig
>
>
>  cp ../surf/rh.inflated.nofix ../surf/rh.inflated
>
> #@# Fix Topology lh Wed Feb 20 19:50:03 EST 2019
>
>  mris_fix_topology 
> -rusage/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/touch/rusage.mris_fix_topology.
> lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 inul_loom2_7T lh
>
> #@# Fix Topology rh Wed Feb 20 19:50:03 EST 2019
>
>  mris_fix_topology 
> -rusage/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/touch/rusage.mris_fix_topology.
> rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 inul_loom2_7T rh
>
> Waiting for PID 8994 of (8994 8997) to complete...
>
>
>
>
>



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Re: [Freesurfer] recon-all -hires

[Bruce Fischl]

Hi MOna


what was your full command line? And can you send us the recon-all.log 
file?


cheers
Bruce
On Thu, 21 Feb 2019, Nasiriavanaki, Zahra wrote:



Dear Freesurfer experts


I was running recon-all command with hires flag for our high resolution fMRI 
data, but it has been in a
constant status since yesterday.

I copied the last few lines that are currently in my terminal. I had the same 
issue with another
subject before, and I had to terminate the recon-all and run it without -hires.

Could you please let me know how I can solve this issue?


Thanks

Mona



#@# Fix Topology Copy rh Wed Feb 20 19:50:00 EST 2019
/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/scripts

 cp ../surf/rh.orig.nofix ../surf/rh.orig 


 cp ../surf/rh.inflated.nofix ../surf/rh.inflated 

#@# Fix Topology lh Wed Feb 20 19:50:03 EST 2019

 mris_fix_topology 
-rusage/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/touch/rusage.mris_fix_topology.
lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 inul_loom2_7T lh 

#@# Fix Topology rh Wed Feb 20 19:50:03 EST 2019

 mris_fix_topology 
-rusage/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/touch/rusage.mris_fix_topology.
rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 inul_loom2_7T rh 

Waiting for PID 8994 of (8994 8997) to complete...




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Re: [Freesurfer] Recon-all Hires Segmentation Failure

[Bruce Fischl]

Hi Gio,

did you check the output of the skull stripping? It is the most likely 
culprit. It's  hard to tell from those images, but if the lateral cortex 
gets significantly darker than more medial stuff (which happens at high 
field) you might need to add some control points in the white matter of the 
region that was excluded. It would also help if you gave us some details of 
the acquisition. What field strength? Was it prescan normalized? Is there a 
body coil?


cheers
Bruce


  On Thu, 11 Jan 2018, Giovana dos Santos Cover wrote:



Dear Freesurfer Developers,

 

I am trying to segment the grey matter and pial surface using the FreeSurfer 
command recon-all with
the hires flag. But even though there is no error while executing my code, when 
I analyze the output
surfaces, the segmentation is missing some areas in the brain (I attached an 
image to show these
brain regions).

 

My command is:

 

recon-all -all -s $SUBJ -hires -i $IMAGE -expert $EXPERT_FILE

 

My expert file contains:

 

mri_em_register -p .5

mris_fix_topology -s 50

mris_inflate -n 100

 

Does anyone have any thoughts on how to troubleshoot my problem?

 

Thanks in advance,

 

Gio.

 

 1. FreeSurfer version: 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
 2. u-name -a: Linux ubuntu 4.4.0-93-generic #116-Ubuntu SMP Fri Aug 11 
21:17:51 UTC 2017 x86_64
x86_64 x86_64 GNU/Linux
[IMAGE]


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Re: [Freesurfer] Recon-all -hires

[Bruce Fischl]

I'm glad to hear it worked out
Bruce
On Tue, 28 Nov 2017, Hwee Ling Lee wrote:


Dear Bruce,
Thanks for your tip. Actually, it didn't work for me. I went to ask one of my 
colleagues, Martin
Reuter, for help, and it turns out that the permission of my files in the 
$FREESURFER_HOME/bin
folder have been changed to 'read only'. Martin helped me to change the files 
in the
$FREESURFER_HOME/bin folder to all executable files by using this command: 
'chmod u+w *'.

Hence, I'm replying to this thread so that I hope this will help others in the 
future with similar
problems.

Thanks again for your patience!

Cheers,
Hweeling


On 23 November 2017 at 16:24, Bruce Fischl  wrote:
  you need to change your path so that

  which recon-all

  gives you the v6 one. something like:

  set path = ($FREESURFER_HOME/bin $path)
  rehash

  where FREESURFER_HOME points to the v6 version
  cheers
  Bruce


  On Wed, 22 Nov 2017, Hwee Ling Lee wrote:

Dear Bruce,

Sorry about the screenshot of text.

You are right that it still uses the older version of recon-all. 
How do I
fix this then?

I can't delete the older version because I don't have access to it 
at all.

Thanks for your patience.

Cheers,
Hweeling


On 22 November 2017 at 15:52, Bruce Fischl 

wrote:
      Hi Hweeling

      please don't send us screenshots of text - either attach the
      file or include text in the email.

      I'm pretty sure you are using an older recon-all script with a
      newer FREESURFER_HOME. Try typing:

      which recon-all

      I bet it points to somewhere other than your V6
      FREESURFER_HOME/bin dir

      cheers
      Bruce


      On Wed, 22 Nov 2017, Hwee Ling Lee wrote:

            Dear Bruce,

            Thanks for your patience. Attached you will find the
            screenshot of my server. In my institute's
            server, there is an older version of freesurfer,
            which I then change to a newer version before
            starting the recon-all.

            I look forward to your reply.

            Thanks.

            Cheers,
            Hweeling



            On 22 November 2017 at 15:31, Bruce Fischl
             wrote:
                  can you send us the recon-all.log?
                  On Wed, 22 Nov 2017, Hwee Ling Lee wrote:

                        Hi Bruce,

                        I downloaded the latest version of
            freesurfer, "CentOS 6 x86_64 (64b)".

                        Cheers,
                        Hweeling


                        On 21 November 2017 at 23:57, Bruce
            Fischl 
                        wrote:
                              oh, this may be a version mismatch
            then. Which version of FS are you
                        using?
                              On Tue, 21 Nov 2017, Hwee Ling Lee
            wrote:

                                    Dear Bruce,
                                    Thanks for your reply.
                                    I checked the folder and did
            not find the file that was
                        requested.

                                    What I have in the average
            folder that has 'RB*.gca' are
                                   
            'RB_all_2016-05-10.vc700.gca' and
                                   
            'RB_all_withskull_2016-05-10.vc700.gca'.
                                    The other file in that
            folder is
                        'RB_all_2008-03-26.mni152.2mm.lta'.

                                    Cheers,
                                    Hweeling

                                    On Nov 21, 2017 18:05,
            "Bruce Fischl"
                         wrote:
                                          Hi Hweeling

                                          what is
            FREESURFER_HOME set to in the environment? Does
                        that file
                                    exist? It is a
 

Re: [Freesurfer] Recon-all -hires

[Hwee Ling Lee]

Dear Bruce,

Thanks for your tip. Actually, it didn't work for me. I went to ask one of
my colleagues, Martin Reuter, for help, and it turns out that the
permission of my files in the $FREESURFER_HOME/bin folder have been changed
to 'read only'. Martin helped me to change the files in the
$FREESURFER_HOME/bin folder to all executable files by using this command:
'chmod u+w *'.

Hence, I'm replying to this thread so that I hope this will help others in
the future with similar problems.

Thanks again for your patience!

Cheers,
Hweeling


On 23 November 2017 at 16:24, Bruce Fischl 
wrote:

> you need to change your path so that
>
> which recon-all
>
> gives you the v6 one. something like:
>
> set path = ($FREESURFER_HOME/bin $path)
> rehash
>
> where FREESURFER_HOME points to the v6 version
>
> cheers
> Bruce
>
>
> On Wed, 22 Nov 2017, Hwee Ling Lee wrote:
>
> Dear Bruce,
>>
>> Sorry about the screenshot of text.
>>
>> You are right that it still uses the older version of recon-all. How do I
>> fix this then?
>>
>> I can't delete the older version because I don't have access to it at all.
>>
>> Thanks for your patience.
>>
>> Cheers,
>> Hweeling
>>
>>
>> On 22 November 2017 at 15:52, Bruce Fischl 
>> wrote:
>>   Hi Hweeling
>>
>>   please don't send us screenshots of text - either attach the
>>   file or include text in the email.
>>
>>   I'm pretty sure you are using an older recon-all script with a
>>   newer FREESURFER_HOME. Try typing:
>>
>>   which recon-all
>>
>>   I bet it points to somewhere other than your V6
>>   FREESURFER_HOME/bin dir
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Wed, 22 Nov 2017, Hwee Ling Lee wrote:
>>
>> Dear Bruce,
>>
>> Thanks for your patience. Attached you will find the
>> screenshot of my server. In my institute's
>> server, there is an older version of freesurfer,
>> which I then change to a newer version before
>> starting the recon-all.
>>
>> I look forward to your reply.
>>
>> Thanks.
>>
>> Cheers,
>> Hweeling
>>
>>
>>
>> On 22 November 2017 at 15:31, Bruce Fischl
>>  wrote:
>>   can you send us the recon-all.log?
>>   On Wed, 22 Nov 2017, Hwee Ling Lee wrote:
>>
>> Hi Bruce,
>>
>> I downloaded the latest version of
>> freesurfer, "CentOS 6 x86_64 (64b)".
>>
>> Cheers,
>> Hweeling
>>
>>
>> On 21 November 2017 at 23:57, Bruce
>> Fischl 
>> wrote:
>>   oh, this may be a version mismatch
>> then. Which version of FS are you
>> using?
>>   On Tue, 21 Nov 2017, Hwee Ling Lee
>> wrote:
>>
>> Dear Bruce,
>> Thanks for your reply.
>> I checked the folder and did
>> not find the file that was
>> requested.
>>
>> What I have in the average
>> folder that has 'RB*.gca' are
>>
>> 'RB_all_2016-05-10.vc700.gca' and
>>
>> 'RB_all_withskull_2016-05-10.vc700.gca'.
>> The other file in that
>> folder is
>> 'RB_all_2008-03-26.mni152.2mm.lta'.
>>
>> Cheers,
>> Hweeling
>>
>> On Nov 21, 2017 18:05,
>> "Bruce Fischl"
>>  wrote:
>>   Hi Hweeling
>>
>>   what is
>> FREESURFER_HOME set to in the environment? Does
>> that file
>> exist? It is a
>>   standard part of our
>> distribution
>>
>>   cheers
>>   Bruce
>>
>>
>>On Tue, 21 Nov 2017,
>> Hwee Ling Lee wrote:
>>
>> Dear all,
>>
>> I have T1 images
>> collected from the 7T MRI scanner.
>>
>> I downloaded the
>> most recent freesurfer software,
>> and followed
>> all
>> instructions to
>>

Re: [Freesurfer] Recon-all -hires

[Bruce Fischl]

you need to change your path so that

which recon-all

gives you the v6 one. something like:

set path = ($FREESURFER_HOME/bin $path)
rehash

where FREESURFER_HOME points to the v6 version
cheers
Bruce


On Wed, 22 Nov 2017, Hwee Ling Lee 
wrote:



Dear Bruce,

Sorry about the screenshot of text.

You are right that it still uses the older version of recon-all. How do I
fix this then?

I can't delete the older version because I don't have access to it at all.

Thanks for your patience.

Cheers,
Hweeling


On 22 November 2017 at 15:52, Bruce Fischl 
wrote:
  Hi Hweeling

  please don't send us screenshots of text - either attach the
  file or include text in the email.

  I'm pretty sure you are using an older recon-all script with a
  newer FREESURFER_HOME. Try typing:

  which recon-all

  I bet it points to somewhere other than your V6
  FREESURFER_HOME/bin dir

  cheers
  Bruce


  On Wed, 22 Nov 2017, Hwee Ling Lee wrote:

Dear Bruce,

Thanks for your patience. Attached you will find the
screenshot of my server. In my institute's
server, there is an older version of freesurfer,
which I then change to a newer version before
starting the recon-all.

I look forward to your reply.

Thanks.

Cheers,
Hweeling



On 22 November 2017 at 15:31, Bruce Fischl
 wrote:
      can you send us the recon-all.log?
      On Wed, 22 Nov 2017, Hwee Ling Lee wrote:

            Hi Bruce,

            I downloaded the latest version of
freesurfer, "CentOS 6 x86_64 (64b)".

            Cheers,
            Hweeling


            On 21 November 2017 at 23:57, Bruce
Fischl 
            wrote:
                  oh, this may be a version mismatch
then. Which version of FS are you
            using?
                  On Tue, 21 Nov 2017, Hwee Ling Lee
wrote:

                        Dear Bruce,
                        Thanks for your reply.
                        I checked the folder and did
not find the file that was
            requested.

                        What I have in the average
folder that has 'RB*.gca' are
                       
'RB_all_2016-05-10.vc700.gca' and
                       
'RB_all_withskull_2016-05-10.vc700.gca'.
                        The other file in that
folder is
            'RB_all_2008-03-26.mni152.2mm.lta'.

                        Cheers,
                        Hweeling

                        On Nov 21, 2017 18:05,
"Bruce Fischl"
             wrote:
                              Hi Hweeling

                              what is
FREESURFER_HOME set to in the environment? Does
            that file
                        exist? It is a
                              standard part of our
distribution

                              cheers
                              Bruce


                               On Tue, 21 Nov 2017,
Hwee Ling Lee wrote:

                                    Dear all,

                                    I have T1 images
collected from the 7T MRI scanner.

                                    I downloaded the
most recent freesurfer software,
            and followed
                        all
                                    instructions to
install the software before using
            it.

                                    I would like to
segment the T1 data using its high
            resolution
                        image, and
                                    also to segment
the hippocampal subfields.

                                    For command, I
use this:

                                    recon-all -all
-s  -hires -i 

                                    However, I get
an error message:

                                    cannot find
           
$FREESURFER_HOME/average/RB_all_2008-03-26.gca

                                    I'm not sure
what I did wrong.

                              

Re: [Freesurfer] Recon-all -hires

[Hwee Ling Lee]

Dear Bruce,

Sorry about the screenshot of text.

You are right that it still uses the older version of recon-all. How do I
fix this then?

I can't delete the older version because I don't have access to it at all.

Thanks for your patience.

Cheers,
Hweeling


On 22 November 2017 at 15:52, Bruce Fischl 
wrote:

> Hi Hweeling
>
> please don't send us screenshots of text - either attach the file or
> include text in the email.
>
> I'm pretty sure you are using an older recon-all script with a newer
> FREESURFER_HOME. Try typing:
>
> which recon-all
>
> I bet it points to somewhere other than your V6 FREESURFER_HOME/bin dir
>
> cheers
> Bruce
>
>
>
> On Wed, 22 Nov 2017, Hwee Ling Lee wrote:
>
> Dear Bruce,
>>
>> Thanks for your patience. Attached you will find the screenshot of my
>> server. In my institute's
>> server, there is an older version of freesurfer, which I then change to a
>> newer version before
>> starting the recon-all.
>>
>> I look forward to your reply.
>>
>> Thanks.
>>
>> Cheers,
>> Hweeling
>>
>>
>>
>> On 22 November 2017 at 15:31, Bruce Fischl 
>> wrote:
>>   can you send us the recon-all.log?
>>   On Wed, 22 Nov 2017, Hwee Ling Lee wrote:
>>
>> Hi Bruce,
>>
>> I downloaded the latest version of freesurfer, "CentOS 6
>> x86_64 (64b)".
>>
>> Cheers,
>> Hweeling
>>
>>
>> On 21 November 2017 at 23:57, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> wrote:
>>   oh, this may be a version mismatch then. Which version
>> of FS are you
>> using?
>>   On Tue, 21 Nov 2017, Hwee Ling Lee wrote:
>>
>> Dear Bruce,
>> Thanks for your reply.
>> I checked the folder and did not find the file
>> that was
>> requested.
>>
>> What I have in the average folder that has
>> 'RB*.gca' are
>> 'RB_all_2016-05-10.vc700.gca' and
>> 'RB_all_withskull_2016-05-10.vc700.gca'.
>> The other file in that folder is
>> 'RB_all_2008-03-26.mni152.2mm.lta'.
>>
>> Cheers,
>> Hweeling
>>
>> On Nov 21, 2017 18:05, "Bruce Fischl"
>>  wrote:
>>   Hi Hweeling
>>
>>   what is FREESURFER_HOME set to in the
>> environment? Does
>> that file
>> exist? It is a
>>   standard part of our distribution
>>
>>   cheers
>>   Bruce
>>
>>
>>On Tue, 21 Nov 2017, Hwee Ling Lee wrote:
>>
>> Dear all,
>>
>> I have T1 images collected from the
>> 7T MRI scanner.
>>
>> I downloaded the most recent
>> freesurfer software,
>> and followed
>> all
>> instructions to install the software
>> before using
>> it.
>>
>> I would like to segment the T1 data
>> using its high
>> resolution
>> image, and
>> also to segment the hippocampal
>> subfields.
>>
>> For command, I use this:
>>
>> recon-all -all -s 
>> -hires -i > dicom T1
>> image frame 1
>> location>
>>
>> However, I get an error message:
>>
>> cannot find
>> $FREESURFER_HOME/average/RB_all_2008-03-26.gca
>>
>> I'm not sure what I did wrong.
>>
>> Also, how can I combine high
>> resolution segmentation
>> and
>> hippocampal
>> subfields segmentation?
>>
>> Could someone please help?
>>
>> Thanks.
>>
>> Best regards,
>> Hweeling
>>
>>
>>
>>
>>
>>   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
>>   

Re: [Freesurfer] Recon-all -hires

[Bruce Fischl]

Hi Hweeling

please don't send us screenshots of text - either attach the file or 
include text in the email.


I'm pretty sure you are using an older recon-all script with a newer 
FREESURFER_HOME. Try typing:


which recon-all

I bet it points to somewhere other than your V6 FREESURFER_HOME/bin dir

cheers
Bruce


On Wed, 22 Nov 2017, Hwee Ling Lee wrote:


Dear Bruce,

Thanks for your patience. Attached you will find the screenshot of my server. 
In my institute's
server, there is an older version of freesurfer, which I then change to a newer 
version before
starting the recon-all.

I look forward to your reply.

Thanks.

Cheers,
Hweeling



On 22 November 2017 at 15:31, Bruce Fischl  wrote:
  can you send us the recon-all.log?
  On Wed, 22 Nov 2017, Hwee Ling Lee wrote:

Hi Bruce,

I downloaded the latest version of freesurfer, "CentOS 6 x86_64 
(64b)".

Cheers,
Hweeling


On 21 November 2017 at 23:57, Bruce Fischl 

wrote:
      oh, this may be a version mismatch then. Which version of FS 
are you
using?
      On Tue, 21 Nov 2017, Hwee Ling Lee wrote:

            Dear Bruce,
            Thanks for your reply.
            I checked the folder and did not find the file that was
requested.

            What I have in the average folder that has 'RB*.gca' are
            'RB_all_2016-05-10.vc700.gca' and
            'RB_all_withskull_2016-05-10.vc700.gca'.
            The other file in that folder is
'RB_all_2008-03-26.mni152.2mm.lta'.

            Cheers,
            Hweeling

            On Nov 21, 2017 18:05, "Bruce Fischl"
 wrote:
                  Hi Hweeling

                  what is FREESURFER_HOME set to in the 
environment? Does
that file
            exist? It is a
                  standard part of our distribution

                  cheers
                  Bruce


                   On Tue, 21 Nov 2017, Hwee Ling Lee wrote:

                        Dear all,

                        I have T1 images collected from the 7T MRI 
scanner.

                        I downloaded the most recent freesurfer 
software,
and followed
            all
                        instructions to install the software before 
using
it.

                        I would like to segment the T1 data using 
its high
resolution
            image, and
                        also to segment the hippocampal subfields.

                        For command, I use this:

                        recon-all -all -s  -hires -i 


                        However, I get an error message:

                        cannot find
$FREESURFER_HOME/average/RB_all_2008-03-26.gca

                        I'm not sure what I did wrong.

                        Also, how can I combine high resolution 
segmentation
and
            hippocampal
                        subfields segmentation?

                        Could someone please help?

                        Thanks.

                        Best regards,
                        Hweeling





                  The information in this e-mail is intended only 
for the
person to whom
            it is
                  addressed. If you believe this e-mail was sent to 
you in
error and the
            e-mail
                  contains patient information, please contact the 
Partners
Compliance
            HelpLine at
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e-mail was
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            in error
                  but does not contain patient information, please 
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but 

Re: [Freesurfer] Recon-all -hires

[Bruce Fischl]

Hi Danny

you need to specify a subject name/id with -s 

cheers
Bruce
On Wed, 22 Nov 2017, 
Danny Deng wrote:



Dear FS developers,
I have problem as follow when I tried file input/output (original images can 
not be identified)

Xues-MacBook-Air:0001 DannyDeng$ recon-all -i im_0001.dcm
ERROR: must specify a subject id
Xues-MacBook-Air:0001 DannyDeng$ recon-all -i IM_0001.dcm -s anon
mkdir: /Applications/freesurfer/subjects/anon: Permission denied
mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied
mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied
cp: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such 
file or directory
cat: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such 
file or directory
INFO: FreeSurfer build stamps do not match
Subject Stamp: 
Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
/Applications/freesurfer/subjects/anon/scripts/patchdir.txt: No such file or 
directory.
Xues-MacBook-Air:0001 DannyDeng$ recon-all -i IM_0001.dcm -s anon
mkdir: /Applications/freesurfer/subjects/anon: Permission denied
mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied
mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied
cp: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such 
file or directory
cat: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such 
file or directory
INFO: FreeSurfer build stamps do not match
Subject Stamp: 
Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
/Applications/freesurfer/subjects/anon/scripts/patchdir.txt: No such file or 
directory.
Xues-MacBook-Air:0001 DannyDeng$ 

Please help.

Thanks.

Best Regards,Danny Deng

  On Nov 22, 2017, at 1:33 AM, Hwee Ling Lee  wrote:

Dear Bruce,
Thanks for your reply.
I checked the folder and did not find the file that was requested.

What I have in the average folder that has 'RB*.gca' are 
'RB_all_2016-05-10.vc700.gca' and
'RB_all_withskull_2016-05-10.vc700.gca'.
The other file in that folder is 'RB_all_2008-03-26.mni152.2mm.lta'.

Cheers,
Hweeling

On Nov 21, 2017 18:05, "Bruce Fischl"  wrote:
  Hi Hweeling

  what is FREESURFER_HOME set to in the environment? Does that file exist? 
It is a
  standard part of our distribution

  cheers
  Bruce


   On Tue, 21 Nov 2017, Hwee Ling Lee wrote:

Dear all,

I have T1 images collected from the 7T MRI scanner.

I downloaded the most recent freesurfer software, and followed all
instructions to install the software before using it.

I would like to segment the T1 data using its high resolution image,
and
also to segment the hippocampal subfields.

For command, I use this:

recon-all -all -s  -hires -i 

However, I get an error message:

cannot find $FREESURFER_HOME/average/RB_all_2008-03-26.gca

I'm not sure what I did wrong.

Also, how can I combine high resolution segmentation and hippocampal
subfields segmentation?

Could someone please help?

Thanks.

Best regards,
Hweeling





  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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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Recon-all -hires

[Bruce Fischl]

can you send us the recon-all.log?
On Wed, 22 Nov 2017, Hwee Ling Lee wrote:


Hi Bruce,

I downloaded the latest version of freesurfer, "CentOS 6 x86_64 (64b)".

Cheers,
Hweeling


On 21 November 2017 at 23:57, Bruce Fischl  wrote:
  oh, this may be a version mismatch then. Which version of FS are you 
using?
  On Tue, 21 Nov 2017, Hwee Ling Lee wrote:

Dear Bruce,
Thanks for your reply.
I checked the folder and did not find the file that was requested.

What I have in the average folder that has 'RB*.gca' are
'RB_all_2016-05-10.vc700.gca' and
'RB_all_withskull_2016-05-10.vc700.gca'.
The other file in that folder is 'RB_all_2008-03-26.mni152.2mm.lta'.

Cheers,
Hweeling

On Nov 21, 2017 18:05, "Bruce Fischl"  
wrote:
      Hi Hweeling

      what is FREESURFER_HOME set to in the environment? Does that 
file
exist? It is a
      standard part of our distribution

      cheers
      Bruce


       On Tue, 21 Nov 2017, Hwee Ling Lee wrote:

            Dear all,

            I have T1 images collected from the 7T MRI scanner.

            I downloaded the most recent freesurfer software, and 
followed
all
            instructions to install the software before using it.

            I would like to segment the T1 data using its high 
resolution
image, and
            also to segment the hippocampal subfields.

            For command, I use this:

            recon-all -all -s  -hires -i 

            However, I get an error message:

            cannot find 
$FREESURFER_HOME/average/RB_all_2008-03-26.gca

            I'm not sure what I did wrong.

            Also, how can I combine high resolution segmentation and
hippocampal
            subfields segmentation?

            Could someone please help?

            Thanks.

            Best regards,
            Hweeling





      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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The information in this e-mail is intended only for the person to whom it is
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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] Recon-all -hires

[Danny Deng]

Dear FS developers,

I have problem as follow when I tried file input/output (original images can 
not be identified)

Xues-MacBook-Air:0001 DannyDeng$ recon-all -i im_0001.dcm
ERROR: must specify a subject id
Xues-MacBook-Air:0001 DannyDeng$ recon-all -i IM_0001.dcm -s anon
mkdir: /Applications/freesurfer/subjects/anon: Permission denied
mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied
mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied
cp: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such 
file or directory
cat: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such 
file or directory
INFO: FreeSurfer build stamps do not match
Subject Stamp: 
Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
/Applications/freesurfer/subjects/anon/scripts/patchdir.txt: No such file or 
directory.
Xues-MacBook-Air:0001 DannyDeng$ recon-all -i IM_0001.dcm -s anon
mkdir: /Applications/freesurfer/subjects/anon: Permission denied
mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied
mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied
cp: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such 
file or directory
cat: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such 
file or directory
INFO: FreeSurfer build stamps do not match
Subject Stamp: 
Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
/Applications/freesurfer/subjects/anon/scripts/patchdir.txt: No such file or 
directory.
Xues-MacBook-Air:0001 DannyDeng$ 

Please help.

Thanks.

Best Regards,
Danny Deng

> On Nov 22, 2017, at 1:33 AM, Hwee Ling Lee  wrote:
> 
> Dear Bruce,
> 
> Thanks for your reply.
> I checked the folder and did not find the file that was requested.
> 
> What I have in the average folder that has 'RB*.gca' are 
> 'RB_all_2016-05-10.vc700.gca' and 'RB_all_withskull_2016-05-10.vc700.gca'.
> The other file in that folder is 'RB_all_2008-03-26.mni152.2mm.lta'.
> 
> Cheers,
> Hweeling
> 
> On Nov 21, 2017 18:05, "Bruce Fischl"  > wrote:
> Hi Hweeling
> 
> what is FREESURFER_HOME set to in the environment? Does that file exist? It 
> is a standard part of our distribution
> 
> cheers
> Bruce
> 
> 
>  On Tue, 21 Nov 2017, Hwee Ling Lee wrote:
> 
> Dear all,
> 
> I have T1 images collected from the 7T MRI scanner.
> 
> I downloaded the most recent freesurfer software, and followed all
> instructions to install the software before using it.
> 
> I would like to segment the T1 data using its high resolution image, and
> also to segment the hippocampal subfields.
> 
> For command, I use this:
> 
> recon-all -all -s  -hires -i  location>
> 
> However, I get an error message:
> 
> cannot find $FREESURFER_HOME/average/RB_all_2008-03-26.gca
> 
> I'm not sure what I did wrong.
> 
> Also, how can I combine high resolution segmentation and hippocampal
> subfields segmentation?
> 
> Could someone please help?
> 
> Thanks.
> 
> Best regards,
> Hweeling
> 
> 
> 
> 
> 
> 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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> 
> 
> 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 
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> but does not contain patient information, please contact the sender and 
> properly
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Re: [Freesurfer] Recon-all -hires

[Hwee Ling Lee]

Hi Bruce,

I downloaded the latest version of freesurfer, "CentOS 6 x86_64 (64b)".

Cheers,
Hweeling


On 21 November 2017 at 23:57, Bruce Fischl 
wrote:

> oh, this may be a version mismatch then. Which version of FS are you using?
>
> On Tue, 21 Nov 2017, Hwee Ling Lee wrote:
>
> Dear Bruce,
>> Thanks for your reply.
>> I checked the folder and did not find the file that was requested.
>>
>> What I have in the average folder that has 'RB*.gca' are
>> 'RB_all_2016-05-10.vc700.gca' and
>> 'RB_all_withskull_2016-05-10.vc700.gca'.
>> The other file in that folder is 'RB_all_2008-03-26.mni152.2mm.lta'.
>>
>> Cheers,
>> Hweeling
>>
>> On Nov 21, 2017 18:05, "Bruce Fischl"  wrote:
>>   Hi Hweeling
>>
>>   what is FREESURFER_HOME set to in the environment? Does that file
>> exist? It is a
>>   standard part of our distribution
>>
>>   cheers
>>   Bruce
>>
>>
>>On Tue, 21 Nov 2017, Hwee Ling Lee wrote:
>>
>> Dear all,
>>
>> I have T1 images collected from the 7T MRI scanner.
>>
>> I downloaded the most recent freesurfer software, and
>> followed all
>> instructions to install the software before using it.
>>
>> I would like to segment the T1 data using its high resolution
>> image, and
>> also to segment the hippocampal subfields.
>>
>> For command, I use this:
>>
>> recon-all -all -s  -hires -i > image frame 1
>> location>
>>
>> However, I get an error message:
>>
>> cannot find $FREESURFER_HOME/average/RB_all_2008-03-26.gca
>>
>> I'm not sure what I did wrong.
>>
>> Also, how can I combine high resolution segmentation and
>> hippocampal
>> subfields segmentation?
>>
>> Could someone please help?
>>
>> Thanks.
>>
>> Best regards,
>> Hweeling
>>
>>
>>
>>
>>
>>   The information in this e-mail is intended only for the person to
>> whom it is
>>   addressed. If you believe this e-mail was sent to you in error and
>> the e-mail
>>   contains patient information, please contact the Partners
>> Compliance HelpLine at
>>   http://www.partners.org/complianceline . If the e-mail was sent to
>> you in error
>>   but does not contain patient information, please contact the sender
>> and properly
>>   dispose of the e-mail.
>>
>>
>>
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Re: [Freesurfer] Recon-all -hires

[Bruce Fischl]

oh, this may be a version mismatch then. Which version of FS are you 
using?

On Tue, 21 Nov 2017, Hwee Ling Lee wrote:


Dear Bruce,
Thanks for your reply.
I checked the folder and did not find the file that was requested.

What I have in the average folder that has 'RB*.gca' are 
'RB_all_2016-05-10.vc700.gca' and
'RB_all_withskull_2016-05-10.vc700.gca'.
The other file in that folder is 'RB_all_2008-03-26.mni152.2mm.lta'.

Cheers,
Hweeling

On Nov 21, 2017 18:05, "Bruce Fischl"  wrote:
  Hi Hweeling

  what is FREESURFER_HOME set to in the environment? Does that file exist? 
It is a
  standard part of our distribution

  cheers
  Bruce


   On Tue, 21 Nov 2017, Hwee Ling Lee wrote:

Dear all,

I have T1 images collected from the 7T MRI scanner.

I downloaded the most recent freesurfer software, and followed all
instructions to install the software before using it.

I would like to segment the T1 data using its high resolution 
image, and
also to segment the hippocampal subfields.

For command, I use this:

recon-all -all -s  -hires -i 

However, I get an error message:

cannot find $FREESURFER_HOME/average/RB_all_2008-03-26.gca

I'm not sure what I did wrong.

Also, how can I combine high resolution segmentation and hippocampal
subfields segmentation?

Could someone please help?

Thanks.

Best regards,
Hweeling





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


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Re: [Freesurfer] Recon-all -hires

[Hwee Ling Lee]

Dear Bruce,

Thanks for your reply.
I checked the folder and did not find the file that was requested.

What I have in the average folder that has 'RB*.gca' are
'RB_all_2016-05-10.vc700.gca' and 'RB_all_withskull_2016-05-10.vc700.gca'.
The other file in that folder is 'RB_all_2008-03-26.mni152.2mm.lta'.

Cheers,
Hweeling

On Nov 21, 2017 18:05, "Bruce Fischl"  wrote:

> Hi Hweeling
>
> what is FREESURFER_HOME set to in the environment? Does that file exist?
> It is a standard part of our distribution
>
> cheers
> Bruce
>
>
>  On Tue, 21 Nov 2017, Hwee Ling Lee wrote:
>
> Dear all,
>>
>> I have T1 images collected from the 7T MRI scanner.
>>
>> I downloaded the most recent freesurfer software, and followed all
>> instructions to install the software before using it.
>>
>> I would like to segment the T1 data using its high resolution image, and
>> also to segment the hippocampal subfields.
>>
>> For command, I use this:
>>
>> recon-all -all -s  -hires -i > location>
>>
>> However, I get an error message:
>>
>> cannot find $FREESURFER_HOME/average/RB_all_2008-03-26.gca
>>
>> I'm not sure what I did wrong.
>>
>> Also, how can I combine high resolution segmentation and hippocampal
>> subfields segmentation?
>>
>> Could someone please help?
>>
>> Thanks.
>>
>> Best regards,
>> Hweeling
>>
>>
>>
>>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] Recon-all -hires

[Bruce Fischl]

Hi Hweeling

what is FREESURFER_HOME set to in the environment? Does that file exist? It 
is a standard part of our distribution

cheers
Bruce


  On 
Tue, 21 Nov 2017, Hwee Ling Lee wrote:

> Dear all,
> 
> I have T1 images collected from the 7T MRI scanner.
> 
> I downloaded the most recent freesurfer software, and followed all
> instructions to install the software before using it.
> 
> I would like to segment the T1 data using its high resolution image, and
> also to segment the hippocampal subfields.
> 
> For command, I use this:
> 
> recon-all -all -s  -hires -i  location>
> 
> However, I get an error message:
> 
> cannot find $FREESURFER_HOME/average/RB_all_2008-03-26.gca
> 
> I'm not sure what I did wrong.
> 
> Also, how can I combine high resolution segmentation and hippocampal
> subfields segmentation?
> 
> Could someone please help?
> 
> Thanks.
> 
> Best regards,
> Hweeling
> 
> 
>
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