Dear Freesurfers,
I am working on the segmentation of mdeft structural images (Siemens
Allegra 3T-acquired) of schizophrenia patients.
I had troubles editing temporal regions (especially superior temporal
gyrus) by adding control points. After re-running the image in the pipeline
(autorecon2-cp)
Greetings Freesurfers!
recon-all -s XXX_SurferOutput exited with ERRORS
These are the errors in the log:
Reading transforms/talairach.m3z
ERROR: cannot find or read transforms/talairach.m3z
ERROR: mri_ca_register with non-zero status 0
I would really appreciate any advice!
Thank you very much
Hello:
I am trying to run two subjects using Tracula. I have created a config
file, and getting the following error:
set: Variable name must begin with a letter.
ERROR: must specify as many DWI dicoms as subjects
I have tried to debug and can't seem to find the source of this problem. My
config
Hi Pietro,
Yes, the filedrop would be fine or you can upload using ftp.
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
-Louis
On Mon, 11 Nov 2013, pietro de rossi wrote:
Dear Freesurfers,
I am working on the segmentation of mdeft structural images (Siemens Allegra
3T-acquired) of
Hi Salil,
please send questions to the free surfer mailing list.
If you used the longitudinal stream for processing the etiv should be the same
in all time points. It is computed in the 'base' = within subject template once
for the entire series.
It seems that you did not run your images throug
ok. is it possible to upload the whole subject folder?
2013/11/11 Louis Nicholas Vinke
> Hi Pietro,
> Yes, the filedrop would be fine or you can upload using ftp.
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
>
> -Louis
>
>
> On Mon, 11 Nov 2013, pietro de rossi wrote:
>
> Dear
Yes, just tar/zip it up first.
On Mon, 11 Nov 2013, pietro de rossi wrote:
ok. is it possible to upload the whole subject folder?
2013/11/11 Louis Nicholas Vinke
Hi Pietro,
Yes, the filedrop would be fine or you can upload using ftp.
https://surfer.nmr.mgh.harvard.edu/fswi
ok thanks!
2013/11/11 Louis Nicholas Vinke
> Yes, just tar/zip it up first.
>
>
> On Mon, 11 Nov 2013, pietro de rossi wrote:
>
> ok. is it possible to upload the whole subject folder?
>>
>>
>> 2013/11/11 Louis Nicholas Vinke
>> Hi Pietro,
>> Yes, the filedrop would be fine or you
Hi Katica
we need to see what happened before that that caused the talairach.mg3z
to not be created.
cheers
Bruce
On Mon, 11 Nov 2013, Boric, Katica A. wrote:
Greetings Freesurfers!
recon-all -s XXX_SurferOutput exited with ERRORS
These are the errors in the log:
Reading transforms/tala
Hi FS experts,
I’m about to run aparcstats2table for a longitudinal study, and I’m wondering
seeing as I’ve already written a longitudinal qdec table that includes subject
IDs under the fsid column, is it necessary to pass -subjects subj1 subj2 subj3
… etc AND the qdec to aparcstats2table or sh
Hello Freesurfer group,
I have a general question about the Freesurfer pipeline when applied to
fMRI BOLD scans.
In general, with heavily atrophied or older individuals, would there be no
necessary corrections to make for atrophy due to the non-linear surface
inflation transformation that is applie
Thank you Martin.
Just to clarify, then it is not valid to compare values of single point
analyses (e.g. hippocampal volume from freesurfer analysis of time point 1
subtracted from hippocampal volume of from freesurfer analysis of time
point 2).
Best wishes,
-Salil
On Mon, Nov 11, 2013 at 7:58
Hi Salil,
of course you can compare values like you say. Why shouldn't you?
The longitudinal stream is used to increase reliability of reported
measures if you have 2 or more images from the same subjects.
Best Martin
On 11/11/2013 12:00 PM, Salil Soman wrote:
Thank you Martin.
Just to cla
To convert an example Choi2012 file to FSL 2mm space in FreeSurfer 5.2, I have
tried both of the mri_vol2vol commands below. The results as shown in freeview
are offset by several voxels from the original. Is there a transform or an
intermediate step that can make this work -- or a different c
looks like mri_ca_register was killed in the middle. How much ram do you
ahve on that machine? What kind of machine is it and what FS version are
you running?
On Mon, 11 Nov 2013, Boric, Katica A. wrote:
> Hi Bruce!
> Thank you very much!
>
>
> An error before that is:
>
> ERROR: mri_ca_regist
Hello Freesurfers,
I am just wondering if there is a generally accepted lower age limit for
running recon-all and getting reliable results? Lack of myelination in most
children below the age of 3 has caused segmentation issues in our dataset.
Is this common? And, if so, has anything been published
Hi Bruce!
Thank you very much! I guess I know what happened now!
Most likely it ran out of RAM, because I was processing 2 MRIs at the same
time... I guess I can't do that!
I am using freesurfer-x86_64-redhat-linux-gnu-stable5-20130513 on a VMware
virtual machine 9.0.2 build-1031769. The physica
you can if you have enough ram, but maybe 8 isn't enough, particularly if
you are doing anything else on the computer at that time
On Mon, 11 Nov
2013, Boric, Katica A. wrote:
> Hi Bruce!
> Thank you very much! I guess I know what happened now!
> Most likely it ran out of RAM, because I was proc
HI,
I succesfully uploaded the files.
Thanks in advance for your help!
Pietro
--
Pietro De Rossi, MD
-
Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento
NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale
Sant'Andrea, V
Hi Laura - First of all, which version of freesurfer do you have? It looks
to me like you've based your config file on the old example file that came
with version 5.1.
Second, could you please convert your bvecs and bvals files to 3 columns
and 1 column, respectively, then run trac-all and sen
Is the Choi2012 volume in fsaverage/mni305 space? If so, then the 2nd
command is the right one. Use mri_binarize with the --match option to
create separate masks.
doug
On 11/11/13 2:24 PM, Kathy L. Pearson wrote:
> To convert an example Choi2012 file to FSL 2mm space in FreeSurfer 5.2, I
> ha
I think you just need the qdec table.
doug
On 11/11/13 11:27 AM, Jonathan Holt wrote:
> Hi FS experts,
>
> I’m about to run aparcstats2table for a longitudinal study, and I’m wondering
> seeing as I’ve already written a longitudinal qdec table that includes
> subject IDs under the fsid column,
No, there is nothing special you need to do. FSFAST will sample halfway
between the white and pial surfaces which will be as good as you can get
for atrophied brains.
doug
On 11/11/13 11:47 AM, Mario Ortega wrote:
Hello Freesurfer group,
I have a general question about the Freesurfer pip
The only way to do what you want is to combine the labels into an
annotation file (mris_label2annot), then run mris_anatomical_stats on
the annot, then you can run aparcstats2table on the output of that. This
may or may not be easier than doing what you are already doing.
doug.
On 11/10/13 3:
Did you check the registrations to see if either or both are inaccurate?
As you point out, the eTIV is based on the registration an not an actual
count of voxels inside the skull. It may be the case that one time point
has more or less neck than the other which could skew the registrations
si
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