Re: [Freesurfer] Question about compare left and right hemi of longitudinal data

[lanbo Wang]

Hi Martin,

I didn't try to run recon-all, I try to run flipped.
The code I used is:
foreach subject (subj_27_2.long.s27_base)
foreach?   surfreg --s $subject --t fsaverage_sym --lh
foreach?   surfreg --s $subject --t fsaverage_sym --lh --xhemi
foreach? end


Thanks,
Lanbo

On Tue, Jan 16, 2018 at 4:46 AM, Martin Reuter 
wrote:

> Hi Lanbo,
>
> what is the exact command you use for this? The problem is that the script
> or your command does not pass the right flags to recon all. Whenever
> recon-all is supposed to work on a longitudinal directory it needs to know
> the base and the long so the recon all command needs to show
>
> -long subj_02_1 s02_base
>
> as part of its arguments. So either adjust your command line, or if the
> recon-all call is performed from within another script, we need to change
> that script (add a -long flag so that the script performs the correct
> recon-all call in those cases when working on a longitudinal time point).
>
> Once you have the left right difference (define on one of the
> hemispheres), you can treat it similar as a thickness map and run it
> through the Matlab LME code. https://surfer.nmr.mgh.harvard.edu/fswiki/
> LinearMixedEffectsModels
>
>
> Best, Martin
>
> Am 27.12.2017 um 16:11 schrieb lanbo Wang:
>
> Thanks for replying me. But I still have two questions.
> Firstly, when I try xhemi on pre-possessed longitudinal data, it showed
> error like this:
> Performing left-right swap of labels
> TR=2300.00, TE=2.98, TI=900.00, flip angle=9.00
> i_ras = (-1, 3.72529e-08, 3.35276e-08)
> j_ras = (-2.6077e-08, -3.72529e-09, -1)
> k_ras = (-1.78814e-07, 1, 6.98492e-10)
> writing to /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/aparc+a
> seg.mgz...
> Wed Dec 20 17:46:35 EST 2017
> recon-all -sb subj_02_1.long.s02_base/xhemi -talairach
>
> ERROR: Are you trying to run or re-run a longitudinal time point?
>If so, please specify the following parameters:
>
>\' -long   \'
>
>where  is the time point id (SAME as cross sectional
>ID) and  is the ID created in the -base run.
>The directory .long. will be created
>automatically or used for output, if it already exists.
>
> Secondly, how I can get the change rate after construct left -right
> registration.
>
> Thanks,
> Lanbo
>
> On Fri, Dec 22, 2017 at 5:40 AM, Martin Reuter <
> mreu...@nmr.mgh.harvard.edu> wrote:
>
>> Hi Lanbo,
>>
>> you could look at longitudinal changes of the left-right difference in
>> volume per ROI. Or do you mean on the cortical thickness map (I have never
>> done that, but probably works similarly, construct left -right
>> registration, compute difference, then run the LME on that).
>>
>> Best, Martin
>>
>> Am 17.12.2017 um 17:54 schrieb lanbo Wang:
>>
>> Hi, all experts.
>> I want to compare changes rate between left and right hemisphere of
>> longitudinal data, How should I do that, how to combine xhemi with two
>> stage or LME?
>>
>> Best,
>> Lanbo
>>
>>
>> ___
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Re: [Freesurfer] Cortical White matter/corpus callisum

[Alan Francis]

Hi Elisabetta -

Yes it is included in the calculation of the cerebral WM. Since the CC is a
WM tract comprising the Forceps Minor and Major, it is part of the WM
calculation.

best,

Alan


On Tue, Jan 16, 2018 at 11:58 AM, Del Re, Elisabetta <
elisabetta_de...@hms.harvard.edu> wrote:

> Alan,
>
> thank you.
>
> Of course, but my question was different:
>
> Is the volume of the corpus callosum included in the calculation of the
> volume of the 'cerebral white matter'? Or does the volume of the cerebral
> white matter not include the volume of the corpus?
>
> My understanding is that the volume of the corpus is included in the
> calculation of the volume of the cerebral white matter.
>
> Can you confirm?
>
> Thank you,
>
> Elisabetta
>
>
>
>
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
> alandarkene...@gmail.com>
> *Sent:* Tuesday, January 16, 2018 11:42 AM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Cortical White matter/corpus callisum
>
> Hello Elisabetta -
>
> The Corpus callosal volumes are included in the ASEG output and not in the
> WM files. They are titled CC_Anterior, CC_Midbody etc.
>
> Best,
>
> Alan
>
> On Mon, Jan 15, 2018 at 2:11 PM, Del Re, Elisabetta <
> elisabetta_de...@hms.harvard.edu> wrote:
>
> Dear experts,
> Is the corpus callosum volume included in the 'cortical White matter'
> volume?
>
> Thank you,
> Best,
> Elisabetta
>
> Get Outlook for iOS
> 
>
>
> --
> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>
> * Alan N. Francis PhD*
> Instructor - Imaging Neuroscience
> Brain Imaging Center
> McLean Hospital
> Harvard Medical School
> 115 Mill Street, Belmont, MA 02478
> al...@bwh.harvard.edu 
> afran...@mclean.harvard.edu
>
>
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*Alan N. Francis PhD*
Instructor - Imaging Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu 
afran...@mclean.harvard.edu


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[Freesurfer] Issues with hippo subfields / amygdala fixed

[Iglesias Gonzalez, Eugenio]

Dear all,
The problems with the hippocampal subfield / nuclei of amygdala module (as well 
as with the brainstem module) in the dev version should now be fixed.
I apologize for the inconvenience these issues might have caused. I rushed to 
leave everything ready right before the winter break and made a mistake when 
committing files to the repository.
I have also updated the wiki:
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala
https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures
Thanks for the patience,
Eugenio
PS: if anyone has success stories with the new tail/body/head segmentation of 
the hippocampus, please share them with me!


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

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[Freesurfer] Issues with hippo subfields / amygdala fixed

[Maksimovskiy, Arkadiy]

Dear Dr. Iglesias,

Could you please let me know what the specific problems were that are fixed? I 
am asking because I have already applied this segmentation, and want to make 
sure that the data is valid.

Thank you so much,
Arkadiy

--
Arkadiy L. Maksimovskiy, Ph.D.
Postdoctoral Research Fellow
McLean Imaging Center, McLean Hospital
Department of Psychiatry, Harvard Medical School
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Re: [Freesurfer] Issues with hippo subfields / amygdala fixed

[Iglesias Gonzalez, Eugenio]

Good point, Arkadiy.
Essentially, the binaries were expecting the Matlab 2014b runtime to be 
present, but the rest of scripts were still assuming Matlab 2012b (those are 
the files that were not committed).
This should only have happened if you downloaded the dev version between 
December 23rd and January 16th, approximately. If your code ran to completion, 
it should be perfectly fine.
Cheers,
/Eugenio

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


From:  on behalf of "Maksimovskiy, 
Arkadiy" 
Reply-To: Freesurfer support list 
Date: Wednesday, 17 January 2018 at 17:12
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Issues with hippo subfields / amygdala fixed

Dear Dr. Iglesias,

Could you please let me know what the specific problems were that are fixed? I 
am asking because I have already applied this segmentation, and want to make 
sure that the data is valid.

Thank you so much,
Arkadiy

--
Arkadiy L. Maksimovskiy, Ph.D.
Postdoctoral Research Fellow
McLean Imaging Center, McLean Hospital
Department of Psychiatry, Harvard Medical School
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[Freesurfer] Cloning Voxel Tool Question

[Maksimovskiy, Arkadiy]

Hi All,

I was wondering if someone might be able to confirm about whether cloning a 
voxel is working right based on my description. My concern stems from the fact 
that when I follow instructions to clone a voxel from a T1 onto the brainmask, 
I click on the brainmask but do not see any immediate indication that the 
voxel(s) have been cloned. This is unlike erasing voxels, when the immediate 
indication is the brainmask dissappearing within the area that is erased. I was 
wondering if someone imght be able to confirm (1) whether this is normal and 
(2) whether there is no way to see if the voxel has been cloned prior to 
rerunning the reconstruction script with the incorporated edits.

Thank you for your help,
Arkadiy
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Re: [Freesurfer] recon-all exited with error

[Trisanna Sprung-Much]

Thanks Bruce. I have uploaded it but I would like to confirm that you
received the ICBM_305.tar. For some reason I was not able to compress it
any further.

To clarify, subjects 205 and now subject 202 have both failed after surface
extraction.

best
Trisanna

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


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


On Tue, Jan 16, 2018 at 3:08 PM, Bruce Fischl 
wrote:

> you can put it on our ftp site:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
> On Tue, 16 Jan
> 2018, Trisanna Sprung-Much
> wrote:
>
> > Hi Bruce
> > Thanks for the speedy reply. Should I attach it here or is there a place
> I can upload it to?
> >
> > best
> > Trisanna
> >
> > --
> > Ph.D. CandidateMcGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
> >   hmmm, I've never seen label2label core dump before. Can you tar,
> gzip and
> >   upload the entire subject dir?
> >   On Tue, 16 Jan 2018, Trisanna Sprung-Much
> >   wrote:
> >
> >   > Hi there
> >   >
> >   > I ran Freesurfer 6.0 on a subject last night and it took about
> 12 hours (seemed to get
> >   to the very end) and then exited with
> >   > errors. I can open my surfaces so I think it ended roughly with
> the atlas labelling. I
> >   attach the recon-all log file here.
> >   >
> >   > best wishes
> >   >
> >   > Trisanna
> >   > --
> >   > Ph.D. CandidateMcGill University
> >   > Integrated Program in Neuroscience
> >   > Psychology
> >   >
> >   >
> >   >
> >   >
> >   ___
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[Freesurfer] Hippocampal Sub-field volume units

[Crawford, Anna]

Hello,


i am using the hippocampal subfield segmentation. I am looking at the results 
in [lr]h.hippoSfVolumes-T1.v10.txt. I saw the following in the FAQs and was 
unsure of what the units were then in the .txt file. Does the .txt file give 
units in mm^3?




  *   The sum of the number of voxels of a given structure multiplied by the 
volume of a voxel is not equal to the volume reported in 
[lr]h.hippoSfVolumes*.txt.

This is because the volumes are computed upon a soft segmentation, rather than 
the discrete labels in [lr]h.hippoSfLabels*.mgz. This is the same that happens 
with the main recon-all stream: if you compute volumes by counting voxels in 
aseg.mgz, you don't get the values reported in aseg.stats.



Thank you,

Anna

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Re: [Freesurfer] Hippocampal Sub-field volume units

[Iglesias Gonzalez, Eugenio]

Short answer: yes, it’s cubic mm.


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


From:  on behalf of "Crawford, Anna" 

Reply-To: Freesurfer support list 
Date: Wednesday, 17 January 2018 at 19:20
To: Freesurfer support list 
Subject: [Freesurfer] Hippocampal Sub-field volume units


Hello,



i am using the hippocampal subfield segmentation. I am looking at the results 
in [lr]h.hippoSfVolumes-T1.v10.txt. I saw the following in the FAQs and was 
unsure of what the units were then in the .txt file. Does the .txt file give 
units in mm^3?




  *   The sum of the number of voxels of a given structure multiplied by the 
volume of a voxel is not equal to the volume reported in 
[lr]h.hippoSfVolumes*.txt.

This is because the volumes are computed upon a soft segmentation, rather than 
the discrete labels in [lr]h.hippoSfLabels*.mgz. This is the same that happens 
with the main recon-all stream: if you compute volumes by counting voxels in 
aseg.mgz, you don't get the values reported in aseg.stats.





Thank you,

Anna

===
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Re: [Freesurfer] Issues with hippo subfields / amygdala fixed

[Maksimovskiy, Arkadiy]

Got it.
Thank you so much for all the information.
Best,
Arkadiy

--
Arkadiy L. Maksimovskiy, Ph.D.
Postdoctoral Research Fellow
McLean Imaging Center, McLean Hospital
Department of Psychiatry, Harvard Medical School
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Re: [Freesurfer] recon-all exited with error

[Bruce Fischl]

Hi Trisanna

there are a bunch of files, but they all look like they are empty:

r--r--r-- 1 ftpftp   0 Jan 17 14:24 ICBM_305.tar
-r--r--r-- 1 ftpftp   0 Jan 17 14:41 ICBM_305.tar.gz
-r--r--r-- 1 ftpftp   0 Jan 17 15:12 icbm-205.tar.gz


cheers
Bruce
On Wed, 
17 Jan 2018, Trisanna Sprung-Much wrote:



Thanks Bruce. I have uploaded it but I would like to confirm that you received 
the ICBM_305.tar. For
some reason I was not able to compress it any further.

To clarify, subjects 205 and now subject 202 have both failed after surface 
extraction.

best
Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Tue, Jan 16, 2018 at 3:08 PM, Bruce Fischl  
wrote:
  you can put it on our ftp site:

  https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
  On Tue, 16 Jan
  2018, Trisanna Sprung-Much
  wrote:

  > Hi Bruce
  > Thanks for the speedy reply. Should I attach it here or is there a 
place I can upload
  it to?
  >
  > best
  > Trisanna
  >
  > --
  > Ph.D. CandidateMcGill University
  > Integrated Program in Neuroscience
  > Psychology
  >
  >
  > On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl 
 wrote:
  >       hmmm, I've never seen label2label core dump before. Can you tar, 
gzip and
  >       upload the entire subject dir?
  >       On Tue, 16 Jan 2018, Trisanna Sprung-Much
  >       wrote:
  >
  >       > Hi there
  >       >
  >       > I ran Freesurfer 6.0 on a subject last night and it took about 
12 hours
  (seemed to get
  >       to the very end) and then exited with
  >       > errors. I can open my surfaces so I think it ended roughly with 
the atlas
  labelling. I
  >       attach the recon-all log file here.
  >       >
  >       > best wishes
  >       >
  >       > Trisanna
  >       > --
  >       > Ph.D. CandidateMcGill University
  >       > Integrated Program in Neuroscience
  >       > Psychology
  >       >
  >       >
  >       >
  >       >
  >       ___
  >       Freesurfer mailing list
  >       Freesurfer@nmr.mgh.harvard.edu
  >       https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  >
  >
  >       The information in this e-mail is intended only for the person to 
whom it is
  >       addressed. If you believe this e-mail was sent to you in error 
and the e-mail
  >       contains patient information, please contact the Partners 
Compliance HelpLine at
  >       http://www.partners.org/complianceline . If the e-mail was sent 
to you in error
  >       but does not contain patient information, please contact the 
sender and properly
  >       dispose of the e-mail.
  >
  >
  >
  >
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Re: [Freesurfer] recon-all exited with error

[Trisanna Sprung-Much]

Sorry, Bruce. ignore my last email. Not sure what happened there.

I now am trying to upload icbm-205.tar.gz (the subject that failed) but I
get the following and it happens over and over. Any idea what the problem
could be?

trisanna@kaplan:~$ cd data-01/freesurfer/freesurfer_6.0/ICBM_305/
trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ls
fsaverage  icbm-109  icbm-118  icbm-127  icbm-142  icbm-202
icbm-102   icbm-110  icbm-119  icbm-131  icbm-143  icbm-202.tar.gz
icbm-103   icbm-111  icbm-120  icbm-133  icbm-144  icbm-203
icbm-104   icbm-112  icbm-121  icbm-135  icbm-146  icbm-204
icbm-105   icbm-113  icbm-122  icbm-137  icbm-150  icbm-205
icbm-106   icbm-114  icbm-123  icbm-139  icbm-158  icbm-205.tar.gz
icbm-107   icbm-115  icbm-125  icbm-140  icbm-200  icbm-206
icbm-108   icbm-117  icbm-126  icbm-141  icbm-201
trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp
surfer.nmr.mgh.harvard.edu
Connected to surfer.nmr.mgh.harvard.edu.
220-This is the Martinos Center Anonymous FTP service. Use of this
site
220-shows implicit consent to our Acceptable Use Policy outlined
at
220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php

220-
220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
220-
220-229 Entering Extended Passive Mode
220-
220-   and nothing happens OR
220-
220-229 Entering Extended Passive Mode
220-500 Bad EPRT protocol.
220-
220-  try issuing the EPSV command prior to GET or PUT.
220-
220
Name (surfer.nmr.mgh.harvard.edu:trisanna): anonymous
331 Please specify the password.
Password:
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd transfer/incoming
250 Directory successfully changed.
ftp> put icbm-205.tar.gz
local: icbm-205.tar.gz remote: icbm-205.tar.gz
200 PORT command successful. Consider using PASV.
425 Failed to establish connection.


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


On Wed, Jan 17, 2018 at 2:01 PM, Trisanna Sprung-Much <
trisanna.sprung-m...@mail.mcgill.ca> wrote:

> Thanks Bruce. I have uploaded it but I would like to confirm that you
> received the ICBM_305.tar. For some reason I was not able to compress it
> any further.
>
> To clarify, subjects 205 and now subject 202 have both failed after
> surface extraction.
>
> best
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Tue, Jan 16, 2018 at 3:08 PM, Bruce Fischl 
> wrote:
>
>> you can put it on our ftp site:
>>
>> https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
>> On Tue, 16 Jan
>> 2018, Trisanna Sprung-Much
>> wrote:
>>
>> > Hi Bruce
>> > Thanks for the speedy reply. Should I attach it here or is there a
>> place I can upload it to?
>> >
>> > best
>> > Trisanna
>> >
>> > --
>> > Ph.D. CandidateMcGill University
>> > Integrated Program in Neuroscience
>> > Psychology
>> >
>> >
>> > On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu> wrote:
>> >   hmmm, I've never seen label2label core dump before. Can you tar,
>> gzip and
>> >   upload the entire subject dir?
>> >   On Tue, 16 Jan 2018, Trisanna Sprung-Much
>> >   wrote:
>> >
>> >   > Hi there
>> >   >
>> >   > I ran Freesurfer 6.0 on a subject last night and it took about
>> 12 hours (seemed to get
>> >   to the very end) and then exited with
>> >   > errors. I can open my surfaces so I think it ended roughly with
>> the atlas labelling. I
>> >   attach the recon-all log file here.
>> >   >
>> >   > best wishes
>> >   >
>> >   > Trisanna
>> >   > --
>> >   > Ph.D. CandidateMcGill University
>> >   > Integrated Program in Neuroscience
>> >   > Psychology
>> >   >
>> >   >
>> >   >
>> >   >
>> >   ___
>> >   Freesurfer mailing list
>> >   Freesurfer@nmr.mgh.harvard.edu
>> >   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> >   The information in this e-mail is intended only for the person to
>> whom it is
>> >   addressed. If you believe this e-mail was sent to you in error
>> and the e-mail
>> >   contains patient information, please contact the Partners
>> Compliance HelpLine at
>> >   http://www.partners.org/complianceline . If the e-mail was sent
>> to you in error
>> >   but does not contain patient information, please contact the
>> sender and properly
>> >   dispose of the e-mail.
>> >
>> >
>> >
>> >
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>
>
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Re: [Freesurfer] recon-all exited with error

[Hoopes, Andrew]

Hi Trisanna,

Try running 'quote PASV' in ftp before running 'put' - that should hopefully 
clear up this issue.

best,
Andrew


On Jan 17, 2018, at 4:03 PM, Trisanna Sprung-Much 
mailto:trisanna.sprung-m...@mail.mcgill.ca>>
 wrote:

Sorry, Bruce. ignore my last email. Not sure what happened there.

I now am trying to upload icbm-205.tar.gz (the subject that failed) but I get 
the following and it happens over and over. Any idea what the problem could be?

trisanna@kaplan:~$ cd data-01/freesurfer/freesurfer_6.0/ICBM_305/
trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ls
fsaverage  icbm-109  icbm-118  icbm-127  icbm-142  icbm-202
icbm-102   icbm-110  icbm-119  icbm-131  icbm-143  icbm-202.tar.gz
icbm-103   icbm-111  icbm-120  icbm-133  icbm-144  icbm-203
icbm-104   icbm-112  icbm-121  icbm-135  icbm-146  icbm-204
icbm-105   icbm-113  icbm-122  icbm-137  icbm-150  icbm-205
icbm-106   icbm-114  icbm-123  icbm-139  icbm-158  icbm-205.tar.gz
icbm-107   icbm-115  icbm-125  icbm-140  icbm-200  icbm-206
icbm-108   icbm-117  icbm-126  icbm-141  icbm-201
trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp [X] 
surfer.nmr.mgh.harvard.edu
Connected to [X] surfer.nmr.mgh.harvard.edu.
220-This is the Martinos Center Anonymous FTP service. Use of this site
220-shows implicit consent to our Acceptable Use Policy outlined at
220-[X]http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php
220-
220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
220-
220-229 Entering Extended Passive Mode
220-
220-   and nothing happens OR
220-
220-229 Entering Extended Passive Mode
220-500 Bad EPRT protocol.
220-
220-  try issuing the EPSV command prior to GET or PUT.
220-
220
Name (surfer.nmr.mgh.harvard.edu:trisanna): 
anonymous
331 Please specify the password.
Password:
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd transfer/incoming
250 Directory successfully changed.
ftp> put icbm-205.tar.gz
local: icbm-205.tar.gz remote: icbm-205.tar.gz
200 PORT command successful. Consider using PASV.
425 Failed to establish connection.


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


On Wed, Jan 17, 2018 at 2:01 PM, Trisanna Sprung-Much 
mailto:trisanna.sprung-m...@mail.mcgill.ca>>
 wrote:
Thanks Bruce. I have uploaded it but I would like to confirm that you received 
the ICBM_305.tar. For some reason I was not able to compress it any further.

To clarify, subjects 205 and now subject 202 have both failed after surface 
extraction.

best
Trisanna

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


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


On Tue, Jan 16, 2018 at 3:08 PM, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:
you can put it on our ftp site:

https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
On Tue, 16 Jan
2018, Trisanna Sprung-Much
wrote:

> Hi Bruce
> Thanks for the speedy reply. Should I attach it here or is there a place I 
> can upload it to?
>
> best
> Trisanna
>
> --
> Ph.D. CandidateMcGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl 
> mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>   hmmm, I've never seen label2label core dump before. Can you tar, gzip 
> and
>   upload the entire subject dir?
>   On Tue, 16 Jan 2018, Trisanna Sprung-Much
>   wrote:
>
>   > Hi there
>   >
>   > I ran Freesurfer 6.0 on a subject last night and it took about 12 
> hours (seemed to get
>   to the very end) and then exited with
>   > errors. I can open my surfaces so I think it ended roughly with the 
> atlas labelling. I
>   attach the recon-all log file here.
>   >
>   > best wishes
>   >
>   > Trisanna
>   > --
>   > Ph.D. CandidateMcGill University
>   > Integrated Program in Neuroscience
>   > Psychology
>   >
>   >
>   >
>   >
>   ___
>   Freesurfer mailing list
>   Freesurfer@nmr.mgh.harvard.edu
>   [X] [X] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>   The information in this e-mail is intended only for the person to whom 
> it is
>   addressed. If you believe this e-mail was sent to you in error and the 
> e-mail
>   contains patient information, please contact the Partners Compliance 
> HelpLine at
>   [X] [X] http://www.partners.org/complianceline . If the e-mail was sent 
> to you in error
>   but does not contain patient information, please contact the sender and 
> properly
>   dispose of the e-mail.
>
>
>
>
___
Freesurfer mail

[Freesurfer] monte-carlo error in longitudinal pipeline

[miracle ozzoude]

Hello Experts,

I am running a paired t-test cortical thickness analysis based on the
instruction on the wiki page (
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis). However, the
monte carlo files weren't not created when i corrected for multiple
comparisons. Below are my script, fsgd files, mc-z log file, and a
screenshot of contrast folder missing mc.z maps. Please can you help me
figure out why the error is happening. Thank you.

Best,
Paul

*Script*:
pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx martrix2=age.mtx

#resample each subjects's left and right hemisphere data to fsavarage.
mris_preproc --target fsaverage --hemi lh --meas thickness --out
lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
mris_preproc --target fsaverage --hemi rh --meas thickness --out
rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff


# #smoothen the concatenated file by 5mm FWHM. --cortex means only smooth
areas in the cortex. N:B. FWHM changes based on study type.
mri_surf2surf --hemi lh --s fsaverage --sval lh.paired-diff.thickness.mgh
--fwhm 5 --cortex --tval lh.paired-diff.thickness.sm05.mgh
mri_surf2surf --hemi rh --s fsaverage --sval rh.paired-diff.thickness.mgh
--fwhm 5 --cortex --tval rh.paired-diff.thickness.sm05.mgh

# #Run GLM analysis
mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C
$martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir
lh.paired-diff.glmdirir
mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C
$martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir
rh.paired-diff.glmdir

# # #Run Clusterwise correction for multiple comparisons using MONTE CARLO.
First create a table for of simulations
mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 1 2 mc-z.abs.2
--sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 1 2 mc-z.abs.2
--sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite

*Fsgd file 1:pairs.fsgd*

GroupDescriptorFile 1

Class ADEX

Input 1000_1 ADEX

Input 1000_2 ADEX

Input 1001_1 ADEX

Input 1001_2 ADEX

Input 1003_1 ADEX

Input 1003_2 ADEX

Input 1005_1 ADEX

Input 1005_2 ADEX

Input 1008_1 ADEX

Input 1008_2 ADEX

Input 1013_1 ADEX

Input 1013_2 ADEX

Input 1014_1 ADEX

Input 1014_2 ADEX

*Fsgd file 2: paired_diff.fsgd*

GroupDescriptorFile 1

Class ADEX

Variables Age

Input 1000 ADEX 72

Input 1001 ADEX 76

Input 1003 ADEX 72

Input 1005 ADEX 80

Input 1008 ADEX 72

Input 1013 ADEX 80

Input 1014 ADEX 80


mc-z.abs.2.mri_glmfit-sim.log
Description: Binary data
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
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