Re: [Freesurfer] Inquiry about error message when run 'Tracula'

[Xiaofu]

Hi Anastasia,
   Yes. I tried to run bedpostx on a stand-alone computer but it is very
slow although it can work well.
Regarding the b-values, we do have some subjects which were scanned in
different protocols a few years ago. If it is possible, please add the
option to the new version of Tracula, or it's even better to let me know
 how can I change the script by myself.
I have updated the new version of freesurfer, so, I don't need to use
nb0 variable anymore. Thanks for your reminder.

Best,
Xiaofu



Best,
Xiaofu


On Wed, May 27, 2015 at 12:20 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Xiaofu - As I said earlier, it is impossible for us to troubleshoot
> problems with every single type of cluster, especially a type we don't
> have. You'll have to troubleshoot it with your cluster admin, or try to run
> bedpostx on a stand-alone computer. About your other questions:
>
> 1. Currently there is no option to have a different set of b-values for
> each subject. Are you using a different scanning protocol for different
> subjects?
>
> 2. The fact that you mention the nb0 variable tells me that you don't have
> the latest version of freesurfer. It is highly recommended that you run
> tracula from the 5.3 version of freesurfer, after also downloading the
> tracula update posted here:
> http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates
> In the newer version, there is no nb0 variable, the program figures it out
> from the b-value file. But again, it is not ideal to have a different
> number of b=0 images for each subject.
>
> Best,
> a.y
>
>
> On Tue, 26 May 2015, Xiaofu wrote:
>
>  Dear Anastasia,
>>   Thanks for your answer. I tried to replace 'bedpostx_mgh' with
>> 'bedpostx'
>> in the shell file 'tract-all' in order to run Tracula in the C2B2 server
>> (Titan cluster). But it failed as well. Is there anyway to run Tracula,
>> i.e., by pass the running error of bedpostx_mgh?
>>Besides, I have two more questions when I set up a configuration file.
>>   1) In the step9 of Tracula tutorial
>> (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula), i.e.,
>> Specify the b-value table, I can only set bvalfile to specify the location
>> of the b-value table. Can I specify a different b value file for each of
>> the
>> scans in the study (with bvallist,for example) besides a single b value
>> file
>> for all scans in the study (with bvalfile).
>>   2) About the number of low-b images.
>> Since I will use 4D nifty images instead of raw DICOMs, I need to set
>> the number of low-b images in the configuration file, i.e., set nb0.  Can
>> I
>> specify a different nb0 value for each of the scans in the study (with
>> nb0list,for example) besides a single nb0 value for all scans in the
>> study.
>>
>> Best,
>> Xiaofu
>>
>> On Fri, May 22, 2015 at 1:35 PM, Anastasia Yendiki
>>  wrote:
>>
>>   Hi Xiaofu - The bedpostx program is not configured to run on any
>>   type of cluster with any type of queueing software. It was
>>   originally written to be run on an SGE cluster with specific
>>   queue names. The bedpostx_mgh is a modified version that also
>>   works on our PBS cluster. Making it work on additional clusters
>>   would require additional tweaks, and it's impossible for us to
>>   make it work on everyone's cluster.
>>
>>   In a future version, I'd like to give the option to simply print
>>   out all the necessary commands, and then it would be up to the
>>   user to figure out how to submit them as jobs on their own
>>   cluster. This is not implemented yet.
>>
>>   a.y
>>
>>   On Tue, 19 May 2015, Xiaofu wrote:
>>
>> Dear Sir/Madam,  I tried to run Tracula in the C2B2
>> server at Columbia University. However, I got the
>> following error message
>> after submitted my job using qsub to the sever. I'd
>> greatly appreciate it if you could help me resolve
>> this problem.
>>
>> WARN: Running FSL's bedbost locally - this might
>> take a while
>> WARN: It is recommended to run this step on a
>> cluster
>> bedpostx_mgh -n 2 /DTIdata/Tracula/3789/dmri
>> subjectdir is /DTIdata/Tracula/3789/dmri
>> Making bedpostx directory structure
>> Queuing preprocessing stages
>> Unable to run job: Job was rejected because job
>> requests unknown queue "short.q".
>> Exiting.
>> Queuing parallel processing stage
>> Unable to run job: Job was rejected because job
>> requests unknown queue "long.q".
>> Exiting.
>> Queuing post processing stage
>> Unable to run job: Job was rejected because job
>> requests unknown queue "long.q".
>> Exiting.
>>
>> Looking forward to hearing from you. Thank you very
>> mu

Re: [Freesurfer] Tksurfer and Tkregister2 in Ubuntu 14.04

[Bruce Fischl]

Hi Reza

can you use freeview for what you want instead? tksurfer and tkmedit are 
deprecated


cheers
Bruce

On Thu, 11 Jun 2015, Reza Rajimehr wrote:


Hi,
Is there any plan by the Freesurfer team to address this well-known bug?

http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35938.html

http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg36193.html

For now the only workaround is to enter values through command-line.

Best,
Reza

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[Freesurfer] Tksurfer and Tkregister2 in Ubuntu 14.04

[Reza Rajimehr]

Hi,

Is there any plan by the Freesurfer team to address this well-known bug?

http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35938.html

http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg36193.html

For now the only workaround is to enter values through command-line.

Best,
Reza
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[Freesurfer] Longitudinal Freesurfer | BA labels does not change

[Pradeep]

Hello All,

I ran the freesurfer longitudinal stream for a subject with three time
points and found that the /stats/lh.BA.stats has remained constant across
all time points where as aseg.stats showed variations.

Sorry if this question is too nieve.

Thanks,
Pradeep
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Re: [Freesurfer] sagittal slices

[Douglas N Greve]

Do you not have the image in something other than analyze? If not, then 
just keep playing with the letters (ie, PIR) until  you get it right. 
Note that you will not know what is left and right unless you have a 
fiducial on the subject
doug

On 06/11/2015 04:19 PM, Kriegel, Jennifer Lynn Sarai wrote:
>
> I used the following command to convert a sagittal slice from analyze 
> to mgz format. The original was acquired in an anterior to 
> posterior/right to left angle of slices. However, while it is 
> converting to an mgz properly, it seems to be giving me a flip upside 
> down, and reverting to transverse orientation. How do I specify for 
> the sagittal slice?
>
> Thanks.
>
> $FREESURFER_HOME/bin/mri_convert \
>
> $SUBJECTS_DIR/fmri35_MPRAGE_o17/fmri35_MPRAGE_o17_0001.img -it analyze 
> --in_orientation PIR \
>
> $SUBJECTS_DIR/fmri35_o17/mri/orig/001.mgz
>
> - Jennifer Lynn Sarai Kriegel
>
> MS in Psychological Sciences, Cognition and Neuroscience Emphasis
>
> Functional Neuroimaging of Memory Lab, Center for Vital Longevity
>
> The University of Texas at Dallas
>
> jlk130...@utdallas.edu 
>
> 
>
> I am looking for a lot of men who have an infinite capacity to not 
> know what can't be done.
>
> - Henry Ford
>
> The important thing is not to stop questioning. Curiosity has its own 
> reason for existing.
>
> - Albert Einstein
>
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] preproc-sess creates files

[Douglas N Greve]

I'll need more information before I can help you. Please review our bug 
reporting page to see what kind of info is needed:

surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


On 06/11/2015 02:44 PM, Park, Jung Mi wrote:
> Hello Freesurfer team
>
> When I ran preprc-sess of dementia patient's fmri, fmcpr.nii. files 
> and register.dof6.dat were not created automatically after 
> preproc-sess. ThusI had to bbregister in two dementia patients manually.
> However recently I did preproc-sess in the another patient, fmcpr.nii 
> and register.dof6.dat were created automatically.
>
> Could you please give me any inform what made the difference in 
> creating the results of preproc-sess using the fmri data?
> Thank you in advance.
> Bests,
>
> Jung Mi
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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[Freesurfer] sagittal slices

[Kriegel, Jennifer Lynn Sarai]

I used the following command to convert a sagittal slice from analyze to mgz 
format. The original was acquired in an anterior to posterior/right to left 
angle of slices. However, while it is converting to an mgz properly, it seems 
to be giving me a flip upside down, and reverting to transverse orientation. 
How do I specify for the sagittal slice?
Thanks.
$FREESURFER_HOME/bin/mri_convert \
$SUBJECTS_DIR/fmri35_MPRAGE_o17/fmri35_MPRAGE_o17_0001.img -it analyze 
--in_orientation PIR \
$SUBJECTS_DIR/fmri35_o17/mri/orig/001.mgz

- Jennifer Lynn Sarai Kriegel
MS in Psychological Sciences, Cognition and Neuroscience Emphasis
Functional Neuroimaging of Memory Lab, Center for Vital Longevity
The University of Texas at Dallas
jlk130...@utdallas.edu

I am looking for a lot of men who have an infinite capacity to not know what 
can't be done.
- Henry Ford

The important thing is not to stop questioning. Curiosity has its own reason 
for existing.
- Albert Einstein

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Re: [Freesurfer] WM Edits not updating in batch

[Allison Moreau]

Hi Kate,

I am having trouble viewing the image. Could you send it as an attachment?

When you say main surface, are you referring to the pial or white surface?

-Allison

On 06/11/2015 03:07 PM, McLaughlin, Katie wrote:

Hello Freesurfer Experts,

I'm trying to troubleshoot a problem where the main surface in our 
brains is not adjusting following white matter edits using Freesurfer 
5.3. To be clear, the procedure here is:


1) Make edits to wm.mgz
2) Run recon-all -3T -mprage -autorecon2-wm -autorecon3

Following this process, what we see is that the main surface in the 
brain still encompasses areas that were deleted from wm.mgz. Here is 
an example (at bottom of the inferior temporal lobe):

Inline image 1


This seems to be true for all the edits we've made on this set of brains.

There are no errors in recon-all.log, and the right brain is being 
recon'd. Files in the surf directory seem to be updated as expected. 
Any idea what we're missing here? We haven't had trouble with this 
process in the past. Any help would be much appreciated!


Thanks,
Kate



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[Freesurfer] WM Edits not updating in batch

[McLaughlin, Katie]

Hello Freesurfer Experts,

I'm trying to troubleshoot a problem where the main surface in our brains is 
not adjusting following white matter edits using Freesurfer 5.3. To be clear, 
the procedure here is:

1) Make edits to wm.mgz
2) Run recon-all -3T -mprage -autorecon2-wm -autorecon3

Following this process, what we see is that the main surface in the brain still 
encompasses areas that were deleted from wm.mgz. Here is an example (at bottom 
of the inferior temporal lobe):
[Inline image 1]


This seems to be true for all the edits we've made on this set of brains.

There are no errors in recon-all.log, and the right brain is being recon'd. 
Files in the surf directory seem to be updated as expected. Any idea what we're 
missing here? We haven't had trouble with this process in the past. Any help 
would be much appreciated!

Thanks,
Kate

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[Freesurfer] working on different workstations

[Martine Fontaine]

Dear Freesurfer team,

I had read a paper a while ago (see attached) on the effects of changing 
workstation type across data.
I was wondering if that is still an issue.

I have a situation where a set of data were processed on a Mac with this 
version of freesurfer:
freesurfer-i386-apple-darwin11.4.2-stable5-20130514

I now need to edit these recons on my workstation, Ubuntu with this version of 
freesurfer:
freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

Is it possible to edit them on Ubuntu and recon them afterward? or do I need to 
start everything from scratch?

And, if I do need to start everything from scratch, does that also mean that 
one set of data from the same study should be processed on the same workstation 
with the same operating system version?

I hope my questions are not too confusing...

Best,
Martine
Martine Fontaine, B.S.
Research Assistant
Department of Child and Adolescent Psychiatry
New York State Psychiatric Institute
Columbia University
1051 Riverside Drive, Unit 74
New York, NY 10032
(646)-774-6072 
Cognitive Development & Neuroimaging Laboratory
http://www.columbiapsychiatry.org/marshlab
http://www.teenbulimiastudy.org
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[Freesurfer] Research Assistant Job, Chicago, IL

[Emily Rogalski]

Research Study Assistant job available at Northwestern University’s
Cognitive Neurology and Alzheimer’s Disease Center in Chicago, IL.



The research assistant will be responsible for analysis of neuroimaging
datasets, in order to contribute to neuroscientific studies of normal aging
and pathological aging. Duties include coordinating PET and MRI scans, and
analyzing the resultant structural and functional imaging data. The RA may
have the opportunity to administer and score neuropsychological tests.
Additional duties include working on graphics for manuscripts and grants or
other general lab responsibilities.

Candidates must have proficiency with computer programming,
ideally with relevant technical languages such as MATLAB or Python. They
must be willing to learn new MRI analysis software and troubleshoot
problems independently. Prior experience with neuroimaging analysis suites
such as Freesurfer, FSL, or SPM would be extremely useful. Relevant
backgrounds would be in Neuroscience, Biology, Psychology, Computer
Science, Mathematics, and Biomedical Engineering.



*Minimum Qualifications: *

   - The candidate must hold a Bachelor degree.
   - Candidate must be fluent in at least one programming language.
   - A two-year commitment is requested.



*Preferred Qualifications: *

   - Experience using Freesurfer or other neuroimaging platforms.


Job ID: 25712
Research Study Assistant
Northwestern University
Chicago Campus

To access the job posting and/or apply for the job click on the link below:

https://nuhr.northwestern.edu/psp/hr91prod_er/EMPLOYEE/HRMS/c/HRS_HRAM.HRS_CE.GBL?Page=HRS_CE_JOB_DTL&Action=A&JobOpeningId=25712&SiteId=1&PostingSeq=1




If you have specific questions please email: e-rogal...@northwestern.edu

To learn more about our center please go to: www.brain.northwestern.edu

Thanks!
-- 
Emily J Rogalski, PhD
Associate Professor
Northwestern University
Cognitive Neurology and Alzheimer's Disease Center (CNADC)
320 E Superior Street
Searle Building 11th Floor
Chicago, IL 60611
312-503-1155 phone
312-908-8789 fax
erogal...@gmail.com
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[Freesurfer] preproc-sess creates files

[Park, Jung Mi]

Hello Freesurfer team

When I ran preprc-sess of dementia patient's fmri, fmcpr.nii. files and 
register.dof6.dat were not created automatically after preproc-sess. Thus I had 
to bbregister in two dementia patients manually.
However recently I did preproc-sess in the another patient, fmcpr.nii and 
register.dof6.dat were created automatically.

Could you please give me any inform what made the difference in creating the 
results of preproc-sess using the fmri data?
Thank you in advance.
Bests,

Jung Mi
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Re: [Freesurfer] selx3avg-sess and monkey data

[Douglas N Greve]

The easy fix is to edit rawfunc2surf-sess and remove the --cortex flag. 
Alternatively, you could run mri_vol2surf yourself from a  script that 
you write. I've fixed this in version 6 to allow turning off the use of 
--cortex.

doug

On 06/09/2015 05:53 PM, Jackie Lam wrote:
> Hi all,
>
> I’ve recently completed surface reconstruction of macaque brain using 
> Sebastian Moeller’s pipeline (http://freesurfer.net/fswiki/MonkeyData) 
> and now I’d like to analyse retinotopic data and display it on the 
> surface. However, when I try running selx3avg-sess, I get this error: 
> “ERROR: cannot determine format of
> /export01/data/jack/monkey/subjects/MM/session1/bold/011/fmcpr.sm0.self.lh” 
>
>
> which might be resulting from this:
>
> "session1 To Surface -
> rawfunc2surf-sess -fwhm 0 -s session1 -d 
> /export01/data/jack/monkey/subjects/MM -fsd bold -hemi lh -self -nolog 
> -update -per-run
> instem fmcpr
> outstem fmcpr.sm0.self.hemi
> --
> 1/1 session1
>   1/1 session1 011 lh -
> Mon Jun  8 16:53:10 EDT 2015
> mri_vol2surf --mov 
> /export01/data/jack/monkey/subjects/MM/session1/bold/masks/brain.nii.gz --reg 
> /export01/data/jack/monkey/subjects/MM/session1/bold/011/register.dof6.dat 
> --trgsubject MM --interp nearest --projfrac 0.5 --hemi lh 
> --o 
> /export01/data/jack/monkey/subjects/MM/session1/bold/011/masks/brain.self.lh.nii.gz
>  
> --noreshape --cortex
> No such file or directory
> mri_vol2surf: could not open label file 
> /export01/data/jack/monkey/subjects/MM/label/lh.cortex.label”
>
> Is there a work around for this? Or is there a way to generate 
> lh.cortex.label without aseg.mgz?
>
> Thanks!
>
> Jack
>
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Read .mgz file matlab

[Bruce Fischl]

and can you load the same volume into freeview?

On Wed, 10 Jun 2015, dgw wrote:

> What command did you type?
>
>
> On Wed, Jun 10, 2015 at 5:32 PM, Mohammed Goryawala  wrote:
>> Hello All,
>>
>> I am trying to read .mgz files into matlab on MacOSX using the MRIread
>> command.
>>
>> It returns me the following error:
>>
>> SWITCH expression must be a scalar
>> or string constant.
>>
>> Error in load_mgh (line 126)
>> switch type
>>
>> Error in MRIread (line 88)
>>   [mri.vol, M, mr_parms, volsz] =
>>   load_mgh(fspec,[],[],headeronly);
>>
>> Error in
>> corticalGMConnectivityMatrixFreeSurfer
>> (line 6)
>> mri = MRIread(MRI_Filename);
>>
>> Thanks
>> Mohammed Goryawala, PhD
>> University of Miami
>>
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Re: [Freesurfer] bad magic number

[Matthew Brett]

Hi,

On Thu, Jun 11, 2015 at 2:09 AM, Jalmar Teeuw  wrote:
> Hi Matthew,
>
> Thanks for getting back at this. We only process data for our users, so I 
> don't have permission to share a sample with you. But I'll ask around to see 
> if I can get a scan for you.
>
> To be honest, we aren't quite sure if the problem is with nibabel (v1.3.0). I 
> tried to reproduce the problem with one of the scan that was causing this 
> problem, but the conversion worked fine for me (same data, same script, 
> different platform). Although recently we had the same issue cropping up 
> again for another user where only part of the data was affected by this 
> problem. All we know is that the description field of the NIFTI header starts 
> at the right offset, the magic number bytes are off by +one byte, and the 
> brain looks skewed; hence the assumption of an extra byte in one of the 
> transform fields.
>
> Alternatively, we were wondering what happens if the content of the 
> description field exceeded 80 characters
>
> descr = "%s;%s;%s;%s" % (
> pr_hdr.general_info['exam_name'],
> pr_hdr.general_info['patient_name'],
> pr_hdr.general_info['exam_date'].replace(' ',''),
> pr_hdr.general_info['protocol_name'])
> nhdr.structarr['descrip'] = descr[:80]
>
> The python code neatly truncates the description to 80 characters. Could it 
> be possible that an extra '\0' null byte gets written to terminate the 
> string, causing the description field to be 81 bytes long?

I am fairly sure that there is no way to extend the structure by 1
byte with that command.  The header is effectively a C structure,
wrapped by numpy, so even if numpy allowed you to overflow the field
length, it would still only overwrite the next field, and should not
extend the structure.

So - any help you can give to debug this would be great - I don't have
any good ideas at the moment...  For example - can you send a header
from an affected file?

Cheers,

Matthew

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Re: [Freesurfer] FS-FAST bbr registration

[Douglas Greve]

No, sorry. You can run tkregister-sess and it will show each one 
sequentially. This is a good idea and it may be possible with the 
transition to freeview.

doug


On 6/10/15 7:16 PM, sabin khadka wrote:
Hi all- Is there a command we can have screenshots (similar to one 
employed in fsl) of fucntional--> structural registration in FSFAST to 
visually check the registration on top of the BBR cost?

Cheers,
Sabin Khadka




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Re: [Freesurfer] orientation flipped after mri_label2vol

[Bruce Fischl]

Hi Stefani

are the axes also flipped if you view in freeview?

cheers
Bruce
On Thu, 11 Jun 2015, 
Stefani O'Donoghue wrote:



Hi Freesurfer, We've carried out the mri_label2vol step for ROIs in one
hemisphere. When opening in ITKsnap the orientations appeared flipped, with
the axial ROIs overlayed onto the coronal orientation, and coronal over the
axial, and the sagittal plane appeared rotated. 

Can anyone help us fix this so we can map our ROIs to our reg file to create
the vol file? Is this in the --proj flag? Also, should the --identity flag
influence this?


Thanks,

Stefani

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Re: [Freesurfer] quantifyHippocampalSubfields.sh fails in the current version of freesurfer-Darwin-snowleopard-i686-dev.tar.gz

[Eugenio Iglesias]

Hi Carl,

the use of quantifyHippocampalSubfields.sh is:

quantifyHippocampalSubfields.sh suffix outputFile [subjectsDirectory]

Simply run 
quantifyHippocampalSubfields.sh T1 test_no-T1.txt
or
quantifyHippocampalSubfields.sh T1 test_no-T1.txt 
/Applications/freesurfer/subjects/RBrain
 and everything should work

Cheers,

/Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


- Original Message -
From: "Carl Anderson" 
To: "Freesurfer support list" 
Sent: Wednesday, June 10, 2015 6:54:55 PM
Subject: [Freesurfer] quantifyHippocampalSubfields.sh fails in the current  
version of freesurfer-Darwin-snowleopard-i686-dev.tar.gz



Hi All, 


I have been using the quantifyHippocampalSubfields.sh from build 20150507 with 
no problems. 


However when I try to run the script in the new build (20150610) it fails if I 
run with the "T1" flag or without. 


here is the result with T1: 



vermisii:RBrain carlanderson$ 
Gathering results from subjects in: 
test_T1.txt 
Using the suffix name: 
T1 
And writing them to: 
subfieldAnalysis_T1_v1.0 
/Applications/freesurfer/bin/quantifyHippocampalSubfields.sh: line 8: cd: 
test_T1.txt: No such file or directory 
failed to do cd test_T1.txt 
vermisii:RBrain carlanderson$ 




if I omit the T1 flag: 



vermisii:RBrain carlanderson$ quantifyHippocampalSubfields.sh 
subfieldAnalysis_T1_v1.0 test_no-T1.txt 
Gathering results from subjects in: 
/Applications/freesurfer/subjects/RBrain 
Using the suffix name: 
subfieldAnalysis_T1_v1.0 
And writing them to: 
test_no-T1.txt 
vermisii:RBrain carlanderson$ 


Hope this helps, 


Carl 



-- 

<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> 

Carl M. Anderson, Ph.D. (mail stop 204) 
Assistant Professor of Psychiatry, 
Harvard Medical School & 
The Neuroimaging Center, 
McLean Hospital 115 Mill St. Belmont, MA 02478 
Ph: 617-855-2972; Fax: 617-855-2770 
e-mail: remfr...@gmail.com ; carl_ander...@hms.harvard.edu 
<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> 
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[Freesurfer] orientation flipped after mri_label2vol

[Stefani O'Donoghue]

Hi Freesurfer,
We've carried out the mri_label2vol step for ROIs in one hemisphere. When
opening in ITKsnap the orientations appeared flipped, with the axial ROIs
overlayed onto the coronal orientation, and coronal over the axial, and the
sagittal plane appeared rotated.

Can anyone help us fix this so we can map our ROIs to our reg file to
create the vol file? Is this in the --proj flag? Also, should the
--identity flag influence this?


Thanks,

Stefani
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[Freesurfer] About zgees function missing link

[Matthew, L. Wong]

Hi,

I was trying to compile freesurfer on an arm machine and I worked my way
through quite a few obstacles. But when I am compiling the package
mri_robust_register, I came across an error which stated that there is a
function zgees_(*) in MyMatrix.cpp being undeclared.

I wonder if anyone knows where is the implementation of this function? I
had tried locking into lapack, blas and vnl, though I did found some
functions names zgees but the variable declaration was different.

Thanks!

Regards,
Matthew
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Re: [Freesurfer] bad magic number

[Jalmar Teeuw]

Hi Matthew,

Thanks for getting back at this. We only process data for our users, so I don't 
have permission to share a sample with you. But I'll ask around to see if I can 
get a scan for you.

To be honest, we aren't quite sure if the problem is with nibabel (v1.3.0). I 
tried to reproduce the problem with one of the scan that was causing this 
problem, but the conversion worked fine for me (same data, same script, 
different platform). Although recently we had the same issue cropping up again 
for another user where only part of the data was affected by this problem. All 
we know is that the description field of the NIFTI header starts at the right 
offset, the magic number bytes are off by +one byte, and the brain looks 
skewed; hence the assumption of an extra byte in one of the transform fields.

Alternatively, we were wondering what happens if the content of the description 
field exceeded 80 characters

descr = "%s;%s;%s;%s" % (
pr_hdr.general_info['exam_name'],
pr_hdr.general_info['patient_name'],
pr_hdr.general_info['exam_date'].replace(' ',''),
pr_hdr.general_info['protocol_name'])
nhdr.structarr['descrip'] = descr[:80]

The python code neatly truncates the description to 80 characters. Could it be 
possible that an extra '\0' null byte gets written to terminate the string, 
causing the description field to be 81 bytes long?

Cheers,
Jalmar

> On 10 Jun 2015, at 18:42, Matthew Brett  wrote:
> 
> Hi,
> 
>> We had the same problem with importing scans into Freesurfer that had been
>> converted from PAR/REC to NIFTI using nipy. The problem only affected a
>> subset of the data. When visualising the data with Fiji the brain appeared
>> highly skewed. Upon closer inspection of the header data of the NIFTI file we
>> discovered that there was an extra byte somewhere between the description
>> fields and the magic number sequence, causing the magic number to be
>> misinterpreted by Freesurfer. The extra byte was somewhere in the
>> transformation matrix that is located between the description field and the
>> magic number, but it's impossible to fix unless you know what the content of
>> the transformation matrix is supposed to be. However, when using dcm2nii,
>> part of mricron (from what I understand a newer version of mricro), to
>> convert our PAR/REC files to NIFTI the problem disappeared.
> 
> I'm the maintainer of nibabel so I guess I'm responsible for this
> bug...   Can someone point me to a PAR / REC file that causes this
> problem?   Private off-list is fine, but an image I can share for
> automated testing would be even better...
> 
> Cheers,
> 
> Matthew
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