Re: [Freesurfer] Unable to run recon all

2020-01-20 Thread Sahil Bajaj 
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Hi Dough,

I was just wondering if you got a chance to look at the files I
uploaded on Martinos
Center File Drop . I would
really appreciate any help/updates.

Best,
Sahil

On Mon, Jan 6, 2020 at 11:50 AM Sahil Bajaj  wrote:

> Hi Dough,
>
> I just uploaded one of the files on Martinos Center File Drop
> . I hope that works !
> (Somehow, uploading through ftp was taking too long).
>
> Thanks.
>
> On Mon, Jan 6, 2020 at 11:19 AM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> It is not clear why it failed for these subjects (always happens at the
>> same place). Can you upload one of them for me to take a look at? here
>> are the instructions
>>
>>  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 1/6/20 11:49 AM, Sahil Bajaj wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Hi Dough,
>> >
>> > I finished recon -all on about 515 subjects and I get error in 11 out
>> > of 515 subjects. Here I am attaching recon-all.log files of all those
>> > 11 subjects. I would really appreciate your help in fixing these errors.
>> >
>> > Thanks,
>> > Sahil
>> >
>> > On Thu, Jan 2, 2020 at 10:03 AM Greve, Douglas N.,Ph.D.
>> > mailto:dgr...@mgh.harvard.edu>> wrote:
>> >
>> > Can you send the recon-all.log file? You sent the .error file
>> >
>> > On 12/20/2019 10:13 AM, Sahil Bajaj wrote:
>> >>
>> >> External Email - Use Caution
>> >>
>> >> Hello FS experts,
>> >>
>> >> I am trying to run recon all on about 100 subjects. But one out
>> >> of 100 subjects finishes recon all with error, and doesn't
>> >> complete the process. Here I am attaching recon all log for your
>> >> reference. Also, before installing freesurfer on MAC Catalina, I
>> >> ran sudo spctl - -master -disable
>> >>
>> >> I would really appreciate any help in resolving this.
>> >>
>> >> Thanks,
>> >> Sahil
>> >> 1) FreeSurfer version:
>> >>
>> >> freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
>> >>
>> >> 2) Platform: MACOS Catalina
>> >> 3) recon-all.log: see attached
>> >>
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[Freesurfer] Register for the Spring FreeSurfer Course Tomorrow

2020-01-20 Thread Morgan, Leah 
Hi everyone,

This is a reminder that registration for the Spring 2020 FreeSurfer course will 
open TOMORROW (Tuesday, January 21st) at 10:30am EST!

At that time, the link to the registration page will appear on the course 
website:
https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription

The four-day course will run from March 30th through April 2nd, 2020 at the 
Massachusetts General Hospital Martinos Center for Biomedical Imaging in 
Charlestown, Massachusetts. The schedule for this course has not been finalized 
but an example schedule can be found on the course website:
https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription

How to get a spot in the course
-Easy! Register on the day we open registration & submit an accepted form of 
payment by the deadline.

Some reasons why people are unable to attend the course:
-Waiting too long to register. The 50 seats in the course usually fill up 
within a day or two.
-Waiting too long before requesting a check from their institution. (Make sure 
you put in the request for a check immediately *after* you register.)
-Not realizing cash payments must also be made by the deadline. (MoneyGram or 
Western Union transfers are accepted as well as personal deliveries.)
-Booking flights, sending in payment, and/or just showing up without 
registering for the course or moving up from the waiting list!

For questions about the course, you'll likely find answers on the course 
website. If you don't find what you're looking for, feel free to email the 
course organizers at freesurfer...@gmail.com.

If you would like to hear about future course dates, sign up for the course 
mailing list 
here.
--
FreeSurfer Course Organizers
Massachusetts General Hospital
Athinoula A. Martinos Center for Biomedical Imaging
Bldg. 149, 13th Street
Charlestown, MA 02129
Phone: (617) 726-6598
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Re: [Freesurfer] freesurfer fornix

2020-01-20 Thread Annink, K.V. 
External Email - Use Caution

Dear all,

I have a question about the fornix segmentation. First I have used the comment 
mri_cc -f to create fornix.mgz. After all files were created, I have used 
mri_segstats to create the stats file. Is this correct? In the output file the 
nvoxes and volume are the same.

Thank you for your help.

Kind regards,
Kim

# VoxelVolume_mm3 1
# TableCol  1 ColHeader Index
# TableCol  1 FieldName Index
# TableCol  1 Units NA
# TableCol  2 ColHeader SegId
# TableCol  2 FieldName Segmentation Id
# TableCol  2 Units NA
# TableCol  3 ColHeader NVoxels
# TableCol  3 FieldName Number of Voxels
# TableCol  3 Units unitless
# TableCol  4 ColHeader Volume_mm3
# TableCol  4 FieldName Volume
# TableCol  4 Units mm^3
# TableCol  5 ColHeader StructName
# TableCol  5 FieldName Structure Name
# TableCol  5 Units NA
# NRows 1
# NTableCols 5
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName
  1 250   465  465.0  Fornix

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[Freesurfer] Fwd: Input PET images for PetSurfer Analysis

2020-01-20 Thread Ferraro, Pilar 
External Email - Use Caution

Dear Freesurfer experts,
I am starting a new analysis using PetSurfer to evaluate the effect of 
different PVC corrections on brain metabolism in a set of patients.
I have already analyzed all the T1 MRI data using the normal stream, however I 
have never worked on PET data before.
I have the original DICOMS from a static PET acquisition but I’d like to know 
more about the preprocessing steps needed for these PET data.
I am thinking I should simply convert PET DICOMS to NifTI, normalize them to a 
standard template and then smooth them with 8- mm full width at half maximum 
Gaussian Kernel to obtain the input images for the PetSurfer analysis.
Am I correct or should I add further preprocessing steps?
Thanks,

Pilar






Il giorno 16 gen 2020, alle ore 6:00 PM, 
freesurfer-requ...@nmr.mgh.harvard.edu
 ha scritto:

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Today's Topics:

  1. Qdec and TkSurfer input boxes (Marcos Martins da Silva)
  2. FreeSurfer analyses in MatLab (Graduate Imaging)
  3. Re: Oval shape in average subject inflated (Marina Fern?ndez)
  4. Segfault in mris_topo_fixer (Christian O'Reilly, Dr)
  5. Re: Segfault in mris_topo_fixer (Hoopes, Andrew)
  6. Segmentation Fault during recon-all using FLAIR Image
 (Swanson,Clayton)


--

Message: 1
Date: Wed, 15 Jan 2020 14:02:26 -0300
From: Marcos Martins da Silva 
Subject: [Freesurfer] Qdec and TkSurfer input boxes
To: freesurfer 
Message-ID:

Content-Type: text/plain; charset="utf-8"

   External Email - Use Caution

Hi! I use FreeSurfer 6.0 over CentOS 7. I have just notice a problem with
input/entry/edit boxes in Qdec and TkSurfer. I can see box content, click
inside the box and even select the content but it seems read only: I can't
change it. So it is impossible to see the scatter plot from a specific
vertex inputing its number. Any clue about what happened and how to fix it?
Thank you for your attention.
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Message: 2
Date: Wed, 15 Jan 2020 16:08:12 -0500
From: Graduate Imaging 
Subject: [Freesurfer] FreeSurfer analyses in MatLab
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:

Content-Type: text/plain; charset="utf-8"

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Hello,

I recently ran a vertex wise analysis on two different projects the first
had three groups with three co-variates that looked at if group membership
was associated with brain volume. The second project had two groups with
three co-variates looking at psychiatric x BMI interaction effect on brain
volume. I'm interested in running ROI analyses in matlab to ensure the same
matrices were used.

To run the ROI analyses I'm going to important the design matrix from the
vertex wise analysis and use the fast_glmfit and fast_fratio commands as
shown below:
X = load('Xg.dat');
C = load('C.dat');
y = load('ROI.dat'); text file containing participant ROI values from the
DKT atlas.
[beta rvar] = fast_glmfit(y,X);
[F pvalues] = fast_fratio(beta,X,rvar,C

My first question is the beta values that are calculated from fast_glmfit
are unstandardized is there anyway way to have it compute standardized
values?

My second question is when I ran the ROI analyses looking at the diagnosis
x BMI interaction effect it outputs an array of beta values for each
regressor. In addition to each groups beta value (for BMI) I'm interested
in the beta value of the interaction (ie diagnosis x BMI). I was wondering
how do i go about obtaining this? Would I have to create a new matrix with
the interaction term included in it?

If so would the analysis essentially be one group with the diagnosis x BMI
interaction term plus the three co-variates?
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Message: 3
Date: Thu, 16 Jan 2020 12:58:41 +0100
From: Marina Fern?ndez 
Subject: Re: [Freesurfer] Oval shape in average subject inflated
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:

Content-Type: text/plain; charset="utf-8"

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It works! Thank you very much Bruce!
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