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Today's Topics:
1. Problem running infant FreeSurfer - failure to create
symbolic link (Fleur Warton)
2. Re: Problem running infant FreeSurfer - failure to create
symbolic link (Tim Sch?fer)
3. Re: Viewing labels in freeview (Wang, Ruopeng)
4. Re: Masking surface overlays and spatial correlations
(Douglas N. Greve)
5. Re: Functional connectivity preprocessing and seed analysis
(Douglas N. Greve)
6. Re: recon-all 7.1.1 (James Hartzell)
7. Re: Functional connectivity preprocessing and seed analysis
(Wenzhen Zhao)
8. Re: Functional connectivity preprocessing and seed analysis
(Douglas N. Greve)
----------------------------------------------------------------------
Message: 1
Date: Mon, 21 Sep 2020 11:51:53 +0200
From: Fleur Warton <fleur.warton@gmail.com>
Subject: [Freesurfer] Problem running infant FreeSurfer - failure to
create symbolic link
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CANGE1NGZK2QiKjwFBzVP4-wyyB6GoD=HkzKdGwc_8_+KWNf1Xw@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hi FreeSurfer team,
I'm trying to run the infant freesurfer (version:
freesurfer-infant-20200205 ) and get the following error:
ln: failed to create symbolic link 'brain.nii.gz': Operation not supported
The command I used was:
infant_recon_all --s 002B --age 0
I think this may have to do with the fact that my subjects_dir is located
on a server (not the computer I'm running FreeSurfer on), since when I ran
the command with the subjects_dir located on my local computer it ran fine
and completed without errors. Unfortunately for space reasons it isn't
possible for me to do that for my entire dataset.
Thanks,
Fleur
--
Fleur Warton
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------------------------------
Message: 2
Date: Mon, 21 Sep 2020 11:59:41 +0200 (CEST)
From: Tim Sch?fer <ts+ml@rcmd.org>
Subject: Re: [Freesurfer] Problem running infant FreeSurfer - failure
to create symbolic link
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <242731556.19971.1600682381375@ox.hosteurope.de>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hi Fleur,
the error:
> ln: failed to create symbolic link 'brain.nii.gz': Operation not supported
sounds like the file system used on the server does not support the creation of symbolic links. Maybe this is a Windows server, and the hard disk in question is formatted using some Windows file system (e.g., NTFS or some FAT flavour)?
You should ask your IT admin on the server whether they can provide a disk with a unix filesysytem (e.g., ext4).
Best,
Tim
> On 09/21/2020 11:51 AM Fleur Warton <fleur.warton@gmail.com> wrote:
>
>
> External Email - Use Caution
>
> Hi FreeSurfer team,
>
> I'm trying to run the infant freesurfer (version:
> freesurfer-infant-20200205 ) and get the following error:
>
> ln: failed to create symbolic link 'brain.nii.gz': Operation not supported
>
> The command I used was:
>
> infant_recon_all --s 002B --age 0
>
> I think this may have to do with the fact that my subjects_dir is located
> on a server (not the computer I'm running FreeSurfer on), since when I ran
> the command with the subjects_dir located on my local computer it ran fine
> and completed without errors. Unfortunately for space reasons it isn't
> possible for me to do that for my entire dataset.
>
> Thanks,
>
> Fleur
> --
>
> Fleur Warton
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Dr. Tim Sch?fer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
------------------------------
Message: 3
Date: Mon, 21 Sep 2020 12:44:42 +0000
From: "Wang, Ruopeng" <RWANG4@mgh.harvard.edu>
Subject: Re: [Freesurfer] Viewing labels in freeview
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <2D069757-C096-46ED-951C-7B015623450B@mgh.harvard.edu>
Content-Type: text/plain; charset="us-ascii"
Hi Bronwyn,
All the values in your label are negative, while in freeview the default threshold is 0. If you change the threshold to a negative value from the GUI, you should see it.
Best,
Ruopeng
On Sep 20, 2020, at 9:35 PM, Bronwyn Overs <b.overs@neura.edu.au<mailto:b.overs@neura.edu.au>> wrote:
External Email - Use Caution
Hi Ruopeng,
Thank you for your reply. I have since tried to open these problematic label files using freeview from FS 7.1.1, but I am still not able to see them on my surface. I now attach one of the two label files with this issue (the other was 6.6MB in size so was too large to send by email).
Kind regards,
Bronwyn Overs
Research Assistant
[X]
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1725
neura.edu.au <http://neura.edu.au/>
Twitter<https://twitter.com/neuraustralia> | Facebook<https://www.facebook.com/NeuroscienceResearchAustralia> | Subscribe<http://www.neura.edu.au/help-research/subscribe>
________________________________
From: "Wang, Ruopeng" <RWANG4@MGH.HARVARD.EDU<mailto:RWANG4@MGH.HARVARD.EDU>>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Sent: Friday, September 18, 2020 10:28:45 PM
Subject: Re: [Freesurfer] Viewing labels in freeview
Hi Bronwyn,
Would it be possible for you to send us the label file? You may also try the latest freeview from FS 7.1.1. A lot of changes and fixes have been made since version 5.3.
Best,
Ruopeng
On Sep 18, 2020, at 2:03 AM, Bronwyn Overs <b.overs@neura.edu.au<mailto:b.overs@neura.edu.au>> wrote:
External Email - Use Caution
Dear freesurfer mailing list,
I generated my own label file from a linear mixed effects model and now I want to view this label file on the surface of fsaverage using freeview. I am able to load the surface and label files successfully from the command line using the following:
freeview -f $SUBJECTS_DIR/fsaverage_mod/surf/lh.inflated:label=lh.volume.stack.R3B.fwhm20.lmem.final.200817.gender.FDR-0001.label
However, once freeview is open and the label file is loaded, I cannot see the label displayed on the surface (screenshot attached). I am currently using freesurfer version 5.3.0.
Can someone please tell me how to make the label file visible on the surface of fsaverage?
Kind regards,
Bronwyn Overs
Research Assistant
<neura-logo-email.png>
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1725
neura.edu.au <http://neura.edu.au/>
Twitter<https://twitter.com/neuraustralia> | Facebook<https://www.facebook.com/NeuroscienceResearchAustralia> | Subscribe<http://www.neura.edu.au/help-research/subscribe>
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------------------------------
Message: 4
Date: Mon, 21 Sep 2020 10:34:37 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Masking surface overlays and spatial
correlations
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <892cd9c2-046e-501b-f085-9466006f6301@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"
On 9/19/2020 10:31 AM, Mason Wells wrote:
>
> ????????External Email - Use Caution
>
> Hi Experts,
>
> I wonder if anyone can give me any advice on a couple of things.
> 1) I have some ICA spatial maps which I have resampled to the surface
> using bbregister and vol2surf. I can load this data in Freeview as a
> generic overlay (see attched). I also have a label file which is a
> combination of several visual areas. What I want to do is use this
> label as a mask and remove any activation from the ICA map overlay
> which falls outside of the label/mask. Is this possible using
> Freesurfer? In FSL I have been using fslmaths with -mas flag.
What form are your labels in? If they are just binary masks, then you
can use mri_mask
>
> 2) My next question is whether it is possible to run spatial
> correlations on the surface. For example, I would like to know how
> well my ICA component maps match with some visual areas labels I have
> created in Freesurfer. In FSL i have been using fslcc to run these
> correlations between my ROIs and the spatial maps in the volume.
You want to compute a correlation coefficient? Or a dice score?
>
> Thanks in advance,
> Mason
>
> *Mason T Wells, MSc*
>
> *PhD student*
>
> School of Optometry?and Vision Sciences
>
> & Cardiff University Brain Research
>
> Imaging?Centre (CUBRIC), School of Psychology
>
> Cardiff University
>
> Cardiff
>
> CF24 4HQ
>
> UK
>
> */Email/*: WellsMT1@cardiff.ac.uk <mailto:WellsMT1@cardiff.ac.uk>
>
> */Tel/*: 02920 879628
>
> /*Web*/: Cardiff University webpage
> <https://www.cardiff.ac.uk/people/research-students/view/974214->
>
>
>
> *Mason T Wells, MSc*
>
> *Myfyriwr PhD*
>
> Yr Ysgol Optometreg?a Gwyddorau?r?Golwg
>
> & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr
> Ysgol Seicoleg
>
> Prifysgol Caerdydd
>
> Heol Maindy
>
> Caerdydd
>
> CF24 4HQ
>
> DU
>
> */E-bost/*: WellsMT1@caerdydd.ac.uk <mailto:WellsMT1@caerdydd.ac.uk>
>
> */Ff?n/*: 02920 879628
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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------------------------------
Message: 5
Date: Mon, 21 Sep 2020 10:47:17 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Functional connectivity preprocessing and
seed analysis
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <cbdfd70d-4224-c7c0-bc76-eae17edefd67@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Does this happen on a lot of your subjects? I'm not entire sure why it
is happening to this one, but one reason may be that there is more torso
(eg, shoulders) than the usual scan. I was able to get it working if I
initialized it by hand. This would be ok for one subject, but you would
not have to do so with many subjects.
On 9/18/2020 3:58 PM, Wenzhen Zhao wrote:
>
> ????????External Email - Use Caution
>
> Dear Douglas,
>
> I uploaded the file and the file name is wenzhen.tar.gz. the file has
> freesurfer_results and template.nii.gz.
>
> Thank you for looking into the problem. Please let me know if you need
> anything.
>
> Best,
> Wenzhen
>
>> On Sep 18, 2020, at 12:40 PM, Douglas N. Greve
>> <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote:
>>
>> I can't figure out what is going on unless I have the data. Can you
>> upload it? All I need is the subject's dir (output of recon-all) and
>> the template.nii.gz. You? can follow the instructions below
>>
>> From the linux command line,
>> Create the file you want to upload, eg,
>> cd $SUBJECTS_DIR
>> tar cvfz subject.tar.gz ./subject
>> Now log? into our anonymous FTP site:
>> ftp surfer.nmr.mgh.harvard.edu <http://surfer.nmr.mgh.harvard.edu>
>> It will ask you for a user name: use "anonymous" (no quotes)
>> It will ask you for a password: use "anonymous" (no quotes)
>> cd transfer/incoming
>> binary
>> put subject.tar.gz
>> Send an email that the file has been and the name of the file.
>>
>>
>> On 9/18/2020 12:15 PM, Wenzhen Zhao wrote:
>>>
>>> ????????External Email - Use Caution
>>>
>>> Dear Douglas,
>>>
>>> Yes, they do look properly oriented to me.one thing I noticed is
>>> that when I switch over coronal view, sagittal view, and axial view,
>>> brains seem to shift back and forth in horizontal direction. If you
>>> see the picture below, brains are not in the same spot. I am not
>>> sure if this is an issue.
>>>
>>> Best,
>>> Wenzhen
>>> <Screen Shot 2020-09-18 at 12.04.54 PM.png>
>>>> On Sep 18, 2020, at 10:47 AM, Douglas Greve <dgreve@mgh.harvard.edu
>>>> <mailto:dgreve@mgh.harvard.edu>> wrote:
>>>>
>>>> Is the fmri scan properly oriented? Eg, run freeview
>>>> template.nii.gz and see of it is oriented correctly in the FV window
>>>>
>>>> On 9/15/20 2:57 PM, Wenzhen Zhao wrote:
>>>>>
>>>>> ????????External Email - Use Caution
>>>>>
>>>
>>>>> Dear Douglas,
>>>>>
>>>>>
>>>>> I am using freesurfer 6. I used following command to register fMRI
>>>>> data to anatomical scan.
>>>>> $ bbregister --mov sess01/rest/001/template.nii.gz --t2 --s
>>>>> subject --lta register.dof6.lta
>>>>>
>>>>> I used following command to visualize the output; red: functional
>>>>> scan; overlaid on orig.mgz structural scan.
>>>>> $ tkregisterfv --mov sess01/rest/001/template.nii.gz --reg
>>>>> register.dof6.lta --surfs
>>>>>
>>>>> It seems like two are not aligning well. Is there any step that I
>>>>> should take to improve?
>>>>> Again, thank you so much for helping.
>>>>>
>>>>> Best,
>>>>> Wenzhen
>>>>>
>>>>>
>>>>>
>>>>> <Screen Shot 2020-09-15 at 2.51.32 PM.png>
>>>>>
>>>>>> On Sep 15, 2020, at 1:47 PM, Douglas N. Greve
>>>>>> <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote:
>>>>>>
>>>>>> What version of FS are you using? Try using bbregister without an
>>>>>> init option. Also make sure you are specifying --t2
>>>>>> And send your full command lines next time
>>>>>>
>>>>>> On 9/15/2020 1:44 PM, Wenzhen Zhao wrote:
>>>>>>>
>>>>>>> ????????External Email - Use Caution
>>>>>>>
>>>>>>> Dear Douglas,
>>>>>>>
>>>>>>> Do you have any recommendation on which registration method to
>>>>>>> use? If I use default or init-spm, I would not get a correct
>>>>>>> orientation. Below is the images I got using the following command:
>>>>>>>
>>>>>>> freeview -v $SUBJECTS_DIR/subject/mri/orig.mgz:visible=0
>>>>>>> sess01/rest/001/template.nii.gz:reg=sess01/rest/register.dof6.lta
>>>>>>> -f $SUBJECTS_DIR/subject/surf/lh.white
>>>>>>> $SUBJECTS_DIR/subject/surf/rh.white -viewport cor -transform-volume
>>>>>>>
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Wenzhen
>>>>>>> <Screen Shot 2020-09-15 at 1.42.34 PM.png>
>>>>>>>> On Sep 15, 2020, at 12:59 PM, Douglas N. Greve
>>>>>>>> <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote:
>>>>>>>>
>>>>>>>> Both do both ways. I would recommend not using the --init-rr
>>>>>>>> option for BOLD images
>>>>>>>>
>>>>>>>> On 9/15/2020 11:42 AM, Wenzhen Zhao wrote:
>>>>>>>>>
>>>>>>>>> ????????External Email - Use Caution
>>>>>>>>>
>>>>>>>>> Dear Douglas,
>>>>>>>>>
>>>>>>>>> Thank you for your quick response. I just have one more question.
>>>>>>>>>
>>>>>>>>> Does the ?both-way? transformation only done through mri_coreg
>>>>>>>>> command that is embedded in preproc-sess command? Or does
>>>>>>>>> ?bbregister ?init-rr ? rigid transformation also does both-way
>>>>>>>>> transformation?
>>>>>>>>>
>>>>>>>>> Best,
>>>>>>>>> Wenzhen
>>>>>>>>>
>>>>>>>>>> On Sep 15, 2020, at 11:34 AM, Douglas N. Greve
>>>>>>>>>> <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 9/15/2020 11:26 AM, Wenzhen Zhao wrote:
>>>>>>>>>>>
>>>>>>>>>>> ????????External Email - Use Caution
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Dear freesurfer developers,
>>>>>>>>>>>
>>>>>>>>>>> I?m attempting to analyze my resting -state fMRI data,
>>>>>>>>>>> and I followed procedures on your functional
>>>>>>>>>>> connectivity page. When I tried to run preprocessing
>>>>>>>>>>> with my data, but it turns out that default mri_coreg
>>>>>>>>>>> did not register my fMRI template volume onto anatomical
>>>>>>>>>>> scan well. So, I went on to register fMRI to anatomical
>>>>>>>>>>> space on my own using bbregister with (init-rr method -
>>>>>>>>>>> rigid transformation). I re-ran preprocessing without
>>>>>>>>>>> registration (-noreg) to correct motion and
>>>>>>>>>>> slice-timing. My commands looked like below:
>>>>>>>>>>> #bbregister ?mov fMRI_template_volume ?bold ?s subject
>>>>>>>>>>> ?init-rr ?lta functional2anatomical.lta
>>>>>>>>>>> #preproc-sess -s sess01 -fsd rest -stc siemens -noreg
>>>>>>>>>>> -surface fsaverage lhrh -surf-fwhm 5 -mni305-2mm
>>>>>>>>>>> -vol-fwhm 0 -per-run -force
>>>>>>>>>>>
>>>>>>>>>>> Then, I configured seeds (ex. Hippocampus), and ran
>>>>>>>>>>> following commands:
>>>>>>>>>>> #fcseed-config -segid 17 ?-fcname left_hippocampus.dat
>>>>>>>>>>> -fsd rest -mean -cfg left_hippocampus.config
>>>>>>>>>>> #fcseed-sess -s sess01 -cfg left_hippocampus.config
>>>>>>>>>>>
>>>>>>>>>>> It did run smoothly, but what I noticed from fcseed-sess
>>>>>>>>>>> script was it was transforming anatomical aseg mask into
>>>>>>>>>>> functional space. I am confused on this part, because
>>>>>>>>>>> during processing step, we only make registration file
>>>>>>>>>>> for transformation from functional space to anatomical
>>>>>>>>>>> space, but fcseed-sess command needs registration file
>>>>>>>>>>> that moves anatomical scan to functional scan.
>>>>>>>>>>>
>>>>>>>>>> Yes, it just inverts the transform to go in the opposite
>>>>>>>>>> direction
>>>>>>>>>>>
>>>>>>>>>>> # Convert segmentation to native functional space (##from fcseed-sess script##)
>>>>>>>>>>>
>>>>>>>>>>> set cmd = (mri_label2vol --seg $seganat \
>>>>>>>>>>>
>>>>>>>>>>> --reg $reg --temp $template --fillthresh $FillThresh \
>>>>>>>>>>>
>>>>>>>>>>> --o $seg --pvf $pvf);
>>>>>>>>>>>
>>>>>>>>>>> echo $cmd | tee -a $LLF
>>>>>>>>>>>
>>>>>>>>>>> Then, Later, during mkanalysis-sess step, the command seems to use functional 2 anatomical transformation. Could you please clarify which registration file it uses to process each step that I talked about above? Do I also need to make anatomical to functional transformation registration?
>>>>>>>>>>>
>>>>>>>>>> No, once it has a transformation in one direction, it has it
>>>>>>>>>> in both directions
>>>>>>>>>>>
>>>>>>>>>>> I deeply appreciate your help.
>>>>>>>>>>>
>>>>>>>>>>> Sincerely,
>>>>>>>>>>>
>>>>>>>>>>> Wenzhen
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Freesurfer mailing list
>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Freesurfer mailing list
>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Freesurfer mailing list
>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Freesurfer mailing list
>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>> _______________________________________________
>>>>>> Freesurfer mailing list
>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>> _______________________________________________
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> _______________________________________________
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Message: 6
Date: Mon, 21 Sep 2020 16:48:16 +0200
From: James Hartzell <james.hartzell@gmail.com>
Subject: Re: [Freesurfer] recon-all 7.1.1
To: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu>,
freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAKA8X405AjTu-=+q33ZTSKui8TDq8ZODSryAk2o5W83sAMQ-5Q@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hi Andrew
recon-all appears to have run successfully in 7.1.1, so thanks again for
all the guidance.
I've just tried to install the matlab runtime for hipp, amyg, brainstem and
thalamic segmentation,
as per
https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime
fs_install_mcr R2014b
the command finished, but indicated a problem with. final renaming requirement:
"On the target computer, append the following to your
DYLD_LIBRARY_PATH environment variable:
/var/folders/kl/72rg80dd57ncd7nc638fwzmh0000gn/T/tmp.0al9EPfQ/install-target/v84/runtime/maci64:/var/folders/kl/72rg80dd57ncd7nc638fwzmh0000gn/T/tmp.0al9EPfQ/install-target/v84/sys/os/maci64:/var/folders/kl/72rg80dd57ncd7nc638fwzmh0000gn/T/tmp.0al9EPfQ/install-target/v84/bin/maci64:
(Sep 21, 2020 16:41:29) Exiting with status 0
(Sep 21, 2020 16:41:29) End - Successful.
Finished
mv: rename /var/folders/kl/72rg80dd57ncd7nc638fwzmh0000gn/T/tmp.0al9EPfQ/install-target/v84
to /Applications/freesurfer/7.1.1/MCRv84: Permission denied
Also, if you could provide guidance for the append step, that would be great.
Cheers
James
On Sat, Sep 19, 2020 at 4:17 PM James Hartzell <james.hartzell@gmail.com>
wrote:
> Hi Andrew
>
> Thanks for the suggestions. I removed freesurfer and reinstalled just
> 7.1.1.
> When I try to run the original patch you suggested I still get permissions
> problems, even with sudo.
>
> (base) jameshartzell@Jamess-MacBook-Pro ~ % which freesurfer
> /Applications/freesurfer/7.1.1/bin/freesurfer
>
> (base) jameshartzell@Jamess-MacBook-Pro freesurfer % cd
> $FREESURFER_HOME/bin
>
> (base) jameshartzell@Jamess-MacBook-Pro bin % sudo mv recon-all
> recon-all.backup
> Password:
>
> (base) jameshartzell@Jamess-MacBook-Pro bin % sudo curl
> https://raw.githubusercontent.com/freesurfer/freesurfer/fs-7.1/scripts/recon-all
> > recon-all
> zsh: permission denied: recon-all
>
> Here's hoping you can send another fix!
>
> Cheers
> James
>
>
>
> --
> James Hartzell, PhD (2x)
> Donostia-San Sebati?n, Spain
> Center for Mind/Brain Sciences (CIMeC), The University of Trento, Italy
> Center for Buddhist Studies, Columbia University, USA
>
>
--
James Hartzell, PhD (2x)
Donostia-San Sebati?n, Spain
Center for Mind/Brain Sciences (CIMeC), The University of Trento, Italy
Center for Buddhist Studies, Columbia University, USA
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------------------------------
Message: 7
Date: Mon, 21 Sep 2020 10:55:00 -0400
From: Wenzhen Zhao <wenzhen.zhao@yale.edu>
Subject: Re: [Freesurfer] Functional connectivity preprocessing and
seed analysis
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAEUgV8oBoVzWfXtqh33tuK=WiYKs2eS89vhADFYEYnnsTMTsQw@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Dear Douglas,
Yes, it happens with almost every subject I have (n=53). Is there a way to
apply the method to all the participants? If you could instruct me on
initializing by hand, I can manually do them on all subjects.
Thank you for your help!
Best,
Wenzhen
On Mon, Sep 21, 2020 at 10:48 AM Douglas N. Greve <dgreve@mgh.harvard.edu>
wrote:
>
>
>
>
>
>
>
>
> Does this happen on a lot of your subjects? I'm not entire sure why
>
> it is happening to this one, but one reason may be that there is
>
> more torso (eg, shoulders) than the usual scan. I was able to get it
>
> working if I initialized it by hand. This would be ok for one
>
> subject, but you would not have to do so with many subjects.
>
>
>
>
>
>
>
>
>
> On 9/18/2020 3:58 PM, Wenzhen Zhao
>
> wrote:
>
>
>
>
>
>
>
>
> External Email - Use
>
> Caution
>
>
> Dear Douglas,
>
>
>
>
>
>
> I uploaded the file and the file name is
>
> wenzhen.tar.gz. the file has freesurfer_results and
>
> template.nii.gz.
>
>
>
>
>
>
>
> Thank you for looking into the problem. Please let
>
> me know if you need anything.
>
>
>
>
>
>
>
> Best,
>
>
> Wenzhen
>
>
>
>
>
>
>
> On Sep 18, 2020, at 12:40 PM, Douglas N. Greve
>
> <dgreve@mgh.harvard.edu>
>
> wrote:
>
>
>
>
>
>
>
> I can't figure out what is going on unless
>
> I have the data. Can you upload it? All I need is the
>
> subject's dir (output of recon-all) and the
>
> template.nii.gz. You can follow the instructions below
>
>
>
>
>
> From the linux command line,
>
>
> Create the file you want to upload, eg,
>
>
> cd $SUBJECTS_DIR
>
>
> tar cvfz subject.tar.gz ./subject
>
>
> Now log into our anonymous FTP site:
>
>
> ftp surfer.nmr.mgh.harvard.edu
>
>
> It will ask you for a user name: use "anonymous" (no
>
> quotes)
>
>
> It will ask you for a password: use "anonymous" (no
>
> quotes)
>
>
> cd transfer/incoming
>
>
> binary
>
>
> put subject.tar.gz
>
>
> Send an email that the file has been and the name of the
>
> file.
>
>
>
>
>
>
>
>
> On 9/18/2020 12:15 PM,
>
> Wenzhen Zhao wrote:
>
>
>
>
>
>
> External Email - Use
>
> Caution
>
>
> Dear Douglas,
>
>
>
>
>
>
> Yes, they do look properly oriented to
>
> me.one thing I noticed is that when I switch over
>
> coronal view, sagittal view, and axial view, brains
>
> seem to shift back and forth in horizontal
>
> direction. If you see the picture below, brains are
>
> not in the same spot. I am not sure if this is an
>
> issue.
>
>
>
>
>
>
>
> Best,
>
>
> Wenzhen
>
>
>
>
> <Screen
>
> Shot 2020-09-18 at 12.04.54 PM.png>
>
>
>
>
> On Sep 18, 2020, at 10:47 AM,
>
> Douglas Greve <dgreve@mgh.harvard.edu>
>
> wrote:
>
>
>
>
>
>
>
> Is the fmri scan properly
>
> oriented? Eg, run freeview template.nii.gz
>
> and see of it is oriented correctly in the
>
> FV window
>
>
>
>
>
> On 9/15/20 2:57
>
> PM, Wenzhen Zhao wrote:
>
>
>
>
>
>
> External
>
> Email - Use Caution
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Dear Douglas,
>
>
>
>
>
>
>
> I am using freesurfer 6. I
>
> used following command to register fMRI
>
> data to anatomical scan.
>
>
> $ bbregister --mov
>
> sess01/rest/001/template.nii.gz --t2 --s
>
> subject --lta register.dof6.lta
>
>
>
>
>
>
>
> I used following command to
>
> visualize the output; red: functional
>
> scan; overlaid on orig.mgz structural
>
> scan.
>
>
> $ tkregisterfv --mov
>
> sess01/rest/001/template.nii.gz --reg
>
> register.dof6.lta --surfs
>
>
>
>
>
>
>
> It seems like two are not
>
> aligning well. Is there any step that I
>
> should take to improve?
>
>
> Again, thank you so much for
>
> helping.
>
>
>
>
>
>
>
> Best,
>
>
> Wenzhen
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> <Screen Shot 2020-09-15 at
>
> 2.51.32 PM.png>
>
>
>
>
>
>
>
> On Sep 15, 2020, at 1:47
>
> PM, Douglas N. Greve <dgreve@mgh.harvard.edu>
>
> wrote:
>
>
>
>
>
>
>
> What version of FS
>
> are you using? Try using
>
> bbregister without an init option.
>
> Also make sure you are specifying
>
> --t2
>
>
> And send your full command lines
>
> next time
>
>
>
>
>
> On
>
> 9/15/2020 1:44 PM, Wenzhen Zhao
>
> wrote:
>
>
>
>
>
>
> External
>
> Email - Use Caution
>
>
> Dear Douglas,
>
>
>
>
>
>
> Do you have any
>
> recommendation on which
>
> registration method to use? If
>
> I use default or init-spm, I
>
> would not get a correct
>
> orientation. Below is the
>
> images I got using the
>
> following command:
>
>
>
>
>
>
>
>
>
> freeview -v
>
> $SUBJECTS_DIR/subject/mri/orig.mgz:visible=0
>
> sess01/rest/001/template.nii.gz:reg=sess01/rest/register.dof6.lta -f
>
> $SUBJECTS_DIR/subject/surf/lh.white
>
> $SUBJECTS_DIR/subject/surf/rh.white -viewport cor -transform-volume
>
>
>
>
>
>
>
>
>
>
>
>
> Thanks,
>
>
> Wenzhen
>
>
> <Screen Shot
>
> 2020-09-15 at 1.42.34
>
> PM.png>
>
>
>
>
> On Sep 15,
>
> 2020, at 12:59 PM,
>
> Douglas N. Greve <dgreve@mgh.harvard.edu>
>
> wrote:
>
>
>
>
>
>
>
> Both do
>
> both ways. I would
>
> recommend not using
>
> the --init-rr option
>
> for BOLD images
>
>
>
>
>
> On
>
> 9/15/2020 11:42 AM,
>
> Wenzhen Zhao wrote:
>
>
>
>
>
>
> External
>
> Email - Use
>
> Caution
>
>
> Dear Douglas,
>
>
>
>
>
>
> Thank
>
> you for your quick
>
> response. I just
>
> have one more
>
> question.
>
>
>
>
>
>
>
> Does
>
> the ?both-way?
>
> transformation
>
> only done through
>
> mri_coreg command
>
> that is embedded
>
> in preproc-sess
>
> command? Or does
>
> ?bbregister
>
> ?init-rr ? rigid
>
> transformation
>
> also does both-way
>
> transformation?
>
>
>
>
>
>
>
> Best,
>
>
> Wenzhen
>
>
>
>
>
>
>
>
>
> On
>
> Sep 15, 2020,
>
> at 11:34 AM,
>
> Douglas N.
>
> Greve <dgreve@mgh.harvard.edu>
>
> wrote:
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> On
>
> 9/15/2020
>
> 11:26 AM,
>
> Wenzhen Zhao
>
> wrote:
>
>
>
>
>
>
> External Email - Use
>
> Caution
>
>
>
>
>
>
>
>
>
>
>
>
>>
>> Dear
>>
>> freesurfer
>>
>> developers,
>>
>>
>>
>>
>>
>>
>> I?m
>>
>> attempting to
>>
>> analyze my
>>
>> resting -state
>>
>> fMRI data, and
>>
>> I followed
>>
>> procedures on
>>
>> your
>>
>> functional
>>
>> connectivity
>>
>> page. When I
>>
>> tried to run
>>
>> preprocessing
>>
>> with my data,
>>
>> but it turns
>>
>> out that
>>
>> default
>>
>> mri_coreg did
>>
>> not register
>>
>> my fMRI
>>
>> template
>>
>> volume onto
>>
>> anatomical
>>
>> scan well. So,
>>
>> I went on to
>>
>> register fMRI
>>
>> to anatomical
>>
>> space on my
>>
>> own using
>>
>> bbregister
>>
>> with (init-rr
>>
>> method - rigid
>>
>> transformation). I re-ran preprocessing without registration (-noreg) to
>>
>> correct motion
>>
>> and
>>
>> slice-timing.
>>
>> My commands
>>
>> looked like
>>
>> below:
>>
>>
>> #bbregister
>>
>> ?mov
>>
>> fMRI_template_volume
>>
>> ?bold ?s
>>
>> subject
>>
>> ?init-rr ?lta
>>
>> functional2anatomical.lta
>>
>>
>> #preproc-sess
>>
>> -s sess01 -fsd
>>
>> rest -stc
>>
>> siemens -noreg
>>
>> -surface
>>
>> fsaverage lhrh
>>
>> -surf-fwhm 5
>>
>> -mni305-2mm
>>
>> -vol-fwhm 0
>>
>> -per-run
>>
>> -force
>>
>>
>>
>>
>>
>>
>>
>> Then,
>>
>> I configured
>>
>> seeds (ex.
>>
>> Hippocampus),
>>
>> and ran
>>
>> following
>>
>> commands:
>>
>>
>> #fcseed-config
>>
>> -segid 17
>>
>> -fcname
>>
>> left_hippocampus.dat
>>
>> -fsd rest
>>
>> -mean -cfg
>>
>> left_hippocampus.config
>>
>>
>> #fcseed-sess
>>
>> -s sess01 -cfg
>>
>> left_hippocampus.config
>>
>>
>>
>>
>>
>>
>>
>> It
>>
>> did run
>>
>> smoothly, but
>>
>> what I noticed
>>
>> from
>>
>> fcseed-sess
>>
>> script was it
>>
>> was
>>
>> transforming
>>
>> anatomical
>>
>> aseg mask into
>>
>> functional
>>
>> space. I am
>>
>> confused on
>>
>> this part,
>>
>> because during
>>
>> processing
>>
>> step, we only
>>
>> make
>>
>> registration
>>
>> file for
>>
>> transformation
>>
>> from
>>
>> functional
>>
>> space to
>>
>> anatomical
>>
>> space, but
>>
>> fcseed-sess
>>
>> command needs
>>
>> registration
>>
>> file that
>>
>> moves
>>
>> anatomical
>>
>> scan to
>>
>> functional
>>
>> scan.
>>
>>
>>
>>
>>
>>
>>
>
>
>
>
>
>
>
> Yes, it just
>
> inverts the
>
> transform to
>
> go in the
>
> opposite
>
> direction
>
>
>
>
>
>
>
>
>
>>
>>
>>
>>
>>
>> # Convert segmentation to native functional space (##from fcseed-sess script##)
>>
>>
>>
>> set cmd = (mri_label2vol --seg $seganat \
>>
>>
>>
>> --reg $reg --temp $template --fillthresh $FillThresh \
>>
>>
>>
>> --o $seg --pvf $pvf);
>>
>>
>>
>> echo $cmd | tee -a $LLF
>>
>>
>>
>> Then, Later, during mkanalysis-sess step, the command seems to use functional 2 anatomical transformation. Could you please clarify which registration file it uses to process each step that I talked about above? Do I also need to make anatomical to functional transformation registration?
>>
>>
>>
>>
>>
>>
>>
>>
>
>
>
>
>
>
>
> No, once it
>
> has a
>
> transformation
>
> in one
>
> direction, it
>
> has it in both
>
> directions
>
>
>
>
>
>
>
>
>
>>
>>
>>
>>
>>
>> I deeply appreciate your help.
>>
>>
>>
>> Sincerely,
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Wenzhen
>>
>>
>>
>>
>>
>>
>>
>>
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
>
> Freesurfer mailing list
>
> Freesurfer@nmr.mgh.harvard.edu
>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
>
>
> Freesurfer
>
> mailing list
>
>
> Freesurfer@nmr.mgh.harvard.edu
>
>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
>
> Freesurfer mailing list
>
> Freesurfer@nmr.mgh.harvard.edu
>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
>
>
> Freesurfer mailing list
>
>
> Freesurfer@nmr.mgh.harvard.edu
>
>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
>
> Freesurfer mailing list
>
> Freesurfer@nmr.mgh.harvard.edu
>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
>
>
> Freesurfer mailing list
>
>
> Freesurfer@nmr.mgh.harvard.edu
>
>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
>
> Freesurfer mailing list
>
> Freesurfer@nmr.mgh.harvard.edu
>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
>
>
> Freesurfer mailing list
>
>
> Freesurfer@nmr.mgh.harvard.edu
>
>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
>
> Freesurfer mailing list
>
> Freesurfer@nmr.mgh.harvard.edu
>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
>
>
> Freesurfer mailing list
>
>
> Freesurfer@nmr.mgh.harvard.edu
>
>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
>
> Freesurfer mailing list
>
> Freesurfer@nmr.mgh.harvard.edu
>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
>
> Freesurfer mailing list
>
> Freesurfer@nmr.mgh.harvard.edu
>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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------------------------------
Message: 8
Date: Mon, 21 Sep 2020 11:34:20 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Functional connectivity preprocessing and
seed analysis
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <c644d4e1-4ac7-430e-6d77-ea7ee3d16da0@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
You can try following this tutorial
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalRegistration_freeview
Eg, run
tkregisterfv --s subject --mov template.nii.gz --regheader --reg
reg.manual.lta
Adjust the registration so that it is relatively close (does not need to
be exact)
Then? run
bbregister --mov template.nii.gz --init-reg reg.manual.lta --reg
register.dof6.lta --t2
On 9/21/2020 10:55 AM, Wenzhen Zhao wrote:
>
> ????????External Email - Use Caution
>
>
> Dear Douglas,
>
> Yes, it happens with almost every subject I have (n=53). Is there a
> way to apply the method to all the participants? If you could instruct
> me on initializing by hand, I can manually do them on all subjects.
>
> Thank you for your help!
>
> Best,
> Wenzhen
> On Mon, Sep 21, 2020 at 10:48 AM Douglas N. Greve
> <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote:
>
>
>
>
>
>
>
>
>
> Does this happen on a lot of your subjects? I'm not entire sure why
>
> it is happening to this one, but one reason may be that there is
>
> more torso (eg, shoulders) than the usual scan. I was able to get it
>
> working if I initialized it by hand. This would be ok for one
>
> subject, but you would not have to do so with many subjects.
>
>
>
>
>
>
>
>
>
> On 9/18/2020 3:58 PM, Wenzhen Zhao
>
> wrote:
>
>
>
>
>>
>>
>>
>>
>> ????????External Email - Use
>>
>> Caution
>>
>>
>>
>> Dear Douglas,
>>
>>
>>
>>
>>
>>
>> I uploaded the file and the file name is
>>
>> wenzhen.tar.gz. the file has freesurfer_results and
>>
>> template.nii.gz.
>>
>>
>>
>>
>>
>>
>>
>> Thank you for looking into the problem. Please let
>>
>> me know if you need anything.
>>
>>
>>
>>
>>
>>
>>
>> Best,
>>
>>
>> Wenzhen
>>
>>
>>
>>
>>
>>>
>>>
>>> On Sep 18, 2020, at 12:40 PM, Douglas N. Greve
>>>
>>> <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>
>>>
>>> wrote:
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> I can't figure out what is going on unless
>>>
>>> I have the data. Can you upload it? All I need is the
>>>
>>> subject's dir (output of recon-all) and the
>>>
>>> template.nii.gz. You? can follow the instructions below
>>>
>>>
>>>
>>>
>>>
>>> From the linux command line,
>>>
>>>
>>> Create the file you want to upload, eg,
>>>
>>>
>>> cd $SUBJECTS_DIR
>>>
>>>
>>> tar cvfz subject.tar.gz ./subject
>>>
>>>
>>> Now log? into our anonymous FTP site:
>>>
>>>
>>> ftp surfer.nmr.mgh.harvard.edu <http://surfer.nmr.mgh.harvard.edu>
>>>
>>>
>>> It will ask you for a user name: use "anonymous" (no
>>>
>>> quotes)
>>>
>>>
>>> It will ask you for a password: use "anonymous" (no
>>>
>>> quotes)
>>>
>>>
>>> cd transfer/incoming
>>>
>>>
>>> binary
>>>
>>>
>>> put subject.tar.gz
>>>
>>>
>>> Send an email that the file has been and the name of the
>>>
>>> file.
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 9/18/2020 12:15 PM,
>>>
>>> Wenzhen Zhao wrote:
>>>
>>>
>>>
>>>
>>>>
>>>>
>>>> ????????External Email - Use
>>>>
>>>> Caution
>>>>
>>>>
>>>>
>>>> Dear Douglas,
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Yes, they do look properly oriented to
>>>>
>>>> me.one thing I noticed is that when I switch over
>>>>
>>>> coronal view, sagittal view, and axial view, brains
>>>>
>>>> seem to shift back and forth in horizontal
>>>>
>>>> direction. If you see the picture below, brains are
>>>>
>>>> not in the same spot. I am not sure if this is an
>>>>
>>>> issue.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Best,
>>>>
>>>>
>>>> Wenzhen
>>>>
>>>>
>>>>
>>>>
>>>> <Screen
>>>>
>>>> Shot 2020-09-18 at 12.04.54 PM.png>
>>>>
>>>>
>>>>>
>>>>>
>>>>> On Sep 18, 2020, at 10:47 AM,
>>>>>
>>>>> Douglas Greve <dgreve@mgh.harvard.edu
>>>>> <mailto:dgreve@mgh.harvard.edu>>
>>>>>
>>>>> wrote:
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Is the fmri scan properly
>>>>>
>>>>> oriented? Eg, run freeview template.nii.gz
>>>>>
>>>>> and see of it is oriented correctly in the
>>>>>
>>>>> FV window
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On 9/15/20 2:57
>>>>>
>>>>> PM, Wenzhen Zhao wrote:
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>>
>>>>>>
>>>>>> ????????External
>>>>>>
>>>>>> Email - Use Caution
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>>
>>>>>>
>>>>>> Dear Douglas,
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> I am using freesurfer 6. I
>>>>>>
>>>>>> used following command to register fMRI
>>>>>>
>>>>>> data to anatomical scan.
>>>>>>
>>>>>>
>>>>>> $ bbregister --mov
>>>>>>
>>>>>> sess01/rest/001/template.nii.gz --t2 --s
>>>>>>
>>>>>> subject --lta register.dof6.lta
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> I used following command to
>>>>>>
>>>>>> visualize the output; red: functional
>>>>>>
>>>>>> scan; overlaid on orig.mgz structural
>>>>>>
>>>>>> scan.
>>>>>>
>>>>>>
>>>>>> $ tkregisterfv --mov
>>>>>>
>>>>>> sess01/rest/001/template.nii.gz --reg
>>>>>>
>>>>>> register.dof6.lta --surfs
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> It seems like two are not
>>>>>>
>>>>>> aligning well. Is there any step that I
>>>>>>
>>>>>> should take to improve?
>>>>>>
>>>>>>
>>>>>> Again, thank you so much for
>>>>>>
>>>>>> helping.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>>
>>>>>> Wenzhen
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> <Screen Shot 2020-09-15 at
>>>>>>
>>>>>> 2.51.32 PM.png>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Sep 15, 2020, at 1:47
>>>>>>>
>>>>>>> PM, Douglas N. Greve <dgreve@mgh.harvard.edu
>>>>>>> <mailto:dgreve@mgh.harvard.edu>>
>>>>>>>
>>>>>>> wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> What version of FS
>>>>>>>
>>>>>>> are you using? Try using
>>>>>>>
>>>>>>> bbregister without an init option.
>>>>>>>
>>>>>>> Also make sure you are specifying
>>>>>>>
>>>>>>> --t2
>>>>>>>
>>>>>>>
>>>>>>> And send your full command lines
>>>>>>>
>>>>>>> next time
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On
>>>>>>>
>>>>>>> 9/15/2020 1:44 PM, Wenzhen Zhao
>>>>>>>
>>>>>>> wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ????????External
>>>>>>>>
>>>>>>>> Email - Use Caution
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Dear Douglas,
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Do you have any
>>>>>>>>
>>>>>>>> recommendation on which
>>>>>>>>
>>>>>>>> registration method to use? If
>>>>>>>>
>>>>>>>> I use default or init-spm, I
>>>>>>>>
>>>>>>>> would not get a correct
>>>>>>>>
>>>>>>>> orientation. Below is the
>>>>>>>>
>>>>>>>> images I got using the
>>>>>>>>
>>>>>>>> following command:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> freeview -v
>>>>>>>>
>>>>>>>> $SUBJECTS_DIR/subject/mri/orig.mgz:visible=0
>>>>>>>>
>>>>>>>> sess01/rest/001/template.nii.gz:reg=sess01/rest/register.dof6.lta
>>>>>>>> -f
>>>>>>>>
>>>>>>>> $SUBJECTS_DIR/subject/surf/lh.white
>>>>>>>>
>>>>>>>> $SUBJECTS_DIR/subject/surf/rh.white -viewport cor
>>>>>>>> -transform-volume
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>>
>>>>>>>> Wenzhen
>>>>>>>>
>>>>>>>>
>>>>>>>> <Screen Shot
>>>>>>>>
>>>>>>>> 2020-09-15 at 1.42.34
>>>>>>>>
>>>>>>>> PM.png>
>>>>>>>>
>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Sep 15,
>>>>>>>>>
>>>>>>>>> 2020, at 12:59 PM,
>>>>>>>>>
>>>>>>>>> Douglas N. Greve <dgreve@mgh.harvard.edu
>>>>>>>>> <mailto:dgreve@mgh.harvard.edu>>
>>>>>>>>>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Both do
>>>>>>>>>
>>>>>>>>> both ways. I would
>>>>>>>>>
>>>>>>>>> recommend not using
>>>>>>>>>
>>>>>>>>> the --init-rr option
>>>>>>>>>
>>>>>>>>> for BOLD images
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On
>>>>>>>>>
>>>>>>>>> 9/15/2020 11:42 AM,
>>>>>>>>>
>>>>>>>>> Wenzhen Zhao wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> ????????External
>>>>>>>>>>
>>>>>>>>>> Email - Use
>>>>>>>>>>
>>>>>>>>>> Caution
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Dear Douglas,
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Thank
>>>>>>>>>>
>>>>>>>>>> you for your quick
>>>>>>>>>>
>>>>>>>>>> response. I just
>>>>>>>>>>
>>>>>>>>>> have one more
>>>>>>>>>>
>>>>>>>>>> question.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Does
>>>>>>>>>>
>>>>>>>>>> the ?both-way?
>>>>>>>>>>
>>>>>>>>>> transformation
>>>>>>>>>>
>>>>>>>>>> only done through
>>>>>>>>>>
>>>>>>>>>> mri_coreg command
>>>>>>>>>>
>>>>>>>>>> that is embedded
>>>>>>>>>>
>>>>>>>>>> in preproc-sess
>>>>>>>>>>
>>>>>>>>>> command? Or does
>>>>>>>>>>
>>>>>>>>>> ?bbregister
>>>>>>>>>>
>>>>>>>>>> ?init-rr ? rigid
>>>>>>>>>>
>>>>>>>>>> transformation
>>>>>>>>>>
>>>>>>>>>> also does both-way
>>>>>>>>>>
>>>>>>>>>> transformation?
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Best,
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Wenzhen
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On
>>>>>>>>>>>
>>>>>>>>>>> Sep 15, 2020,
>>>>>>>>>>>
>>>>>>>>>>> at 11:34 AM,
>>>>>>>>>>>
>>>>>>>>>>> Douglas N.
>>>>>>>>>>>
>>>>>>>>>>> Greve <dgreve@mgh.harvard.edu
>>>>>>>>>>> <mailto:dgreve@mgh.harvard.edu>>
>>>>>>>>>>>
>>>>>>>>>>> wrote:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On
>>>>>>>>>>>
>>>>>>>>>>> 9/15/2020
>>>>>>>>>>>
>>>>>>>>>>> 11:26 AM,
>>>>>>>>>>>
>>>>>>>>>>> Wenzhen Zhao
>>>>>>>>>>>
>>>>>>>>>>> wrote:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> ????????External Email - Use
>>>>>>>>>>>>
>>>>>>>>>>>> Caution
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Dear
>>>>>>>>>>>>
>>>>>>>>>>>> freesurfer
>>>>>>>>>>>>
>>>>>>>>>>>> developers,
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> I?m
>>>>>>>>>>>>
>>>>>>>>>>>> attempting to
>>>>>>>>>>>>
>>>>>>>>>>>> analyze my
>>>>>>>>>>>>
>>>>>>>>>>>> resting -state
>>>>>>>>>>>>
>>>>>>>>>>>> fMRI data, and
>>>>>>>>>>>>
>>>>>>>>>>>> I followed
>>>>>>>>>>>>
>>>>>>>>>>>> procedures on
>>>>>>>>>>>>
>>>>>>>>>>>> your
>>>>>>>>>>>>
>>>>>>>>>>>> functional
>>>>>>>>>>>>
>>>>>>>>>>>> connectivity
>>>>>>>>>>>>
>>>>>>>>>>>> page. When I
>>>>>>>>>>>>
>>>>>>>>>>>> tried to run
>>>>>>>>>>>>
>>>>>>>>>>>> preprocessing
>>>>>>>>>>>>
>>>>>>>>>>>> with my data,
>>>>>>>>>>>>
>>>>>>>>>>>> but it turns
>>>>>>>>>>>>
>>>>>>>>>>>> out that
>>>>>>>>>>>>
>>>>>>>>>>>> default
>>>>>>>>>>>>
>>>>>>>>>>>> mri_coreg did
>>>>>>>>>>>>
>>>>>>>>>>>> not register
>>>>>>>>>>>>
>>>>>>>>>>>> my fMRI
>>>>>>>>>>>>
>>>>>>>>>>>> template
>>>>>>>>>>>>
>>>>>>>>>>>> volume onto
>>>>>>>>>>>>
>>>>>>>>>>>> anatomical
>>>>>>>>>>>>
>>>>>>>>>>>> scan well. So,
>>>>>>>>>>>>
>>>>>>>>>>>> I went on to
>>>>>>>>>>>>
>>>>>>>>>>>> register fMRI
>>>>>>>>>>>>
>>>>>>>>>>>> to anatomical
>>>>>>>>>>>>
>>>>>>>>>>>> space on my
>>>>>>>>>>>>
>>>>>>>>>>>> own using
>>>>>>>>>>>>
>>>>>>>>>>>> bbregister
>>>>>>>>>>>>
>>>>>>>>>>>> with (init-rr
>>>>>>>>>>>>
>>>>>>>>>>>> method - rigid
>>>>>>>>>>>>
>>>>>>>>>>>> transformation). I re-ran preprocessing without
>>>>>>>>>>>> registration (-noreg) to
>>>>>>>>>>>>
>>>>>>>>>>>> correct motion
>>>>>>>>>>>>
>>>>>>>>>>>> and
>>>>>>>>>>>>
>>>>>>>>>>>> slice-timing.
>>>>>>>>>>>>
>>>>>>>>>>>> My commands
>>>>>>>>>>>>
>>>>>>>>>>>> looked like
>>>>>>>>>>>>
>>>>>>>>>>>> below:
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> #bbregister
>>>>>>>>>>>>
>>>>>>>>>>>> ?mov
>>>>>>>>>>>>
>>>>>>>>>>>> fMRI_template_volume
>>>>>>>>>>>>
>>>>>>>>>>>> ?bold ?s
>>>>>>>>>>>>
>>>>>>>>>>>> subject
>>>>>>>>>>>>
>>>>>>>>>>>> ?init-rr ?lta
>>>>>>>>>>>>
>>>>>>>>>>>> functional2anatomical.lta
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> #preproc-sess
>>>>>>>>>>>>
>>>>>>>>>>>> -s sess01 -fsd
>>>>>>>>>>>>
>>>>>>>>>>>> rest -stc
>>>>>>>>>>>>
>>>>>>>>>>>> siemens -noreg
>>>>>>>>>>>>
>>>>>>>>>>>> -surface
>>>>>>>>>>>>
>>>>>>>>>>>> fsaverage lhrh
>>>>>>>>>>>>
>>>>>>>>>>>> -surf-fwhm 5
>>>>>>>>>>>>
>>>>>>>>>>>> -mni305-2mm
>>>>>>>>>>>>
>>>>>>>>>>>> -vol-fwhm 0
>>>>>>>>>>>>
>>>>>>>>>>>> -per-run
>>>>>>>>>>>>
>>>>>>>>>>>> -force
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Then,
>>>>>>>>>>>>
>>>>>>>>>>>> I configured
>>>>>>>>>>>>
>>>>>>>>>>>> seeds (ex.
>>>>>>>>>>>>
>>>>>>>>>>>> Hippocampus),
>>>>>>>>>>>>
>>>>>>>>>>>> and ran
>>>>>>>>>>>>
>>>>>>>>>>>> following
>>>>>>>>>>>>
>>>>>>>>>>>> commands:
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> #fcseed-config
>>>>>>>>>>>>
>>>>>>>>>>>> -segid 17
>>>>>>>>>>>>
>>>>>>>>>>>> ?-fcname
>>>>>>>>>>>>
>>>>>>>>>>>> left_hippocampus.dat
>>>>>>>>>>>>
>>>>>>>>>>>> -fsd rest
>>>>>>>>>>>>
>>>>>>>>>>>> -mean -cfg
>>>>>>>>>>>>
>>>>>>>>>>>> left_hippocampus.config
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> #fcseed-sess
>>>>>>>>>>>>
>>>>>>>>>>>> -s sess01 -cfg
>>>>>>>>>>>>
>>>>>>>>>>>> left_hippocampus.config
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> It
>>>>>>>>>>>>
>>>>>>>>>>>> did run
>>>>>>>>>>>>
>>>>>>>>>>>> smoothly, but
>>>>>>>>>>>>
>>>>>>>>>>>> what I noticed
>>>>>>>>>>>>
>>>>>>>>>>>> from
>>>>>>>>>>>>
>>>>>>>>>>>> fcseed-sess
>>>>>>>>>>>>
>>>>>>>>>>>> script was it
>>>>>>>>>>>>
>>>>>>>>>>>> was
>>>>>>>>>>>>
>>>>>>>>>>>> transforming
>>>>>>>>>>>>
>>>>>>>>>>>> anatomical
>>>>>>>>>>>>
>>>>>>>>>>>> aseg mask into
>>>>>>>>>>>>
>>>>>>>>>>>> functional
>>>>>>>>>>>>
>>>>>>>>>>>> space. I am
>>>>>>>>>>>>
>>>>>>>>>>>> confused on
>>>>>>>>>>>>
>>>>>>>>>>>> this part,
>>>>>>>>>>>>
>>>>>>>>>>>> because during
>>>>>>>>>>>>
>>>>>>>>>>>> processing
>>>>>>>>>>>>
>>>>>>>>>>>> step, we only
>>>>>>>>>>>>
>>>>>>>>>>>> make
>>>>>>>>>>>>
>>>>>>>>>>>> registration
>>>>>>>>>>>>
>>>>>>>>>>>> file for
>>>>>>>>>>>>
>>>>>>>>>>>> transformation
>>>>>>>>>>>>
>>>>>>>>>>>> from
>>>>>>>>>>>>
>>>>>>>>>>>> functional
>>>>>>>>>>>>
>>>>>>>>>>>> space to
>>>>>>>>>>>>
>>>>>>>>>>>> anatomical
>>>>>>>>>>>>
>>>>>>>>>>>> space, but
>>>>>>>>>>>>
>>>>>>>>>>>> fcseed-sess
>>>>>>>>>>>>
>>>>>>>>>>>> command needs
>>>>>>>>>>>>
>>>>>>>>>>>> registration
>>>>>>>>>>>>
>>>>>>>>>>>> file that
>>>>>>>>>>>>
>>>>>>>>>>>> moves
>>>>>>>>>>>>
>>>>>>>>>>>> anatomical
>>>>>>>>>>>>
>>>>>>>>>>>> scan to
>>>>>>>>>>>>
>>>>>>>>>>>> functional
>>>>>>>>>>>>
>>>>>>>>>>>> scan.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Yes, it just
>>>>>>>>>>>
>>>>>>>>>>> inverts the
>>>>>>>>>>>
>>>>>>>>>>> transform to
>>>>>>>>>>>
>>>>>>>>>>> go in the
>>>>>>>>>>>
>>>>>>>>>>> opposite
>>>>>>>>>>>
>>>>>>>>>>> direction
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> # Convert segmentation to native functional space (##from fcseed-sess script##)
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> set cmd = (mri_label2vol --seg $seganat \
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> --reg $reg --temp $template --fillthresh $FillThresh \
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> --o $seg --pvf $pvf);
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> echo $cmd | tee -a $LLF
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Then, Later, during mkanalysis-sess step, the command seems to use functional 2 anatomical transformation. Could you please clarify which registration file it uses to process each step that I talked about above? Do I also need to make anatomical to functional transformation registration?
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> No, once it
>>>>>>>>>>>
>>>>>>>>>>> has a
>>>>>>>>>>>
>>>>>>>>>>> transformation
>>>>>>>>>>>
>>>>>>>>>>> in one
>>>>>>>>>>>
>>>>>>>>>>> direction, it
>>>>>>>>>>>
>>>>>>>>>>> has it in both
>>>>>>>>>>>
>>>>>>>>>>> directions
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> I deeply appreciate your help.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Sincerely,
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Wenzhen
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>
>>>>>>>>>>>> Freesurfer mailing list
>>>>>>>>>>>>
>>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>>>>
>>>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Freesurfer
>>>>>>>>>>>
>>>>>>>>>>> mailing list
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
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>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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