Re: [Freesurfer] Freesurfer/Freeview help

[Abbie McNulty]

Hello,

Just a couple more questions that would be great if you could answer in
explanation form:

How do people develop finite element models from brain MRI?
How do people learn and implement the software on an example data set?

Abbie

On Tue, Jul 5, 2016 at 9:42 AM, Abbie McNulty  wrote:

> Hello,
>
> Just a couple more questions that would be great if you could answer in
> explanation form:
>
> How do people develop finite element models from brain MRI?
> How do people learn and implement the software on an example data set?
>
> Abbie
>
> On Mon, Jun 27, 2016 at 6:37 PM, Bruce Fischl 
> wrote:
>
>> Hi Abbie
>>
>> you just use the recon-all script from the command line:
>>
>> recon-all \
>> -i  \
>> -sd  \
>> -s  \
>> -all
>>
>> this will take 5-20 hours and at the end will create and populate a
>> directory tree with segmented volumes and surfaces
>> cheers
>> Bruce
>>
>> On Mon, 27 Jun
>> 2016, Abbie McNulty wrote:
>>
>> > Hi Bruce,
>> > I am trying to create a mesh of the MRI scans, eventually with imported
>> > scans, but for now just using the information available through the
>> > software. How do you work these voxel segmentations? I'm just very new
>> with
>> > the software.
>> >
>> > Say I import an MRI scan, and I want to cortically segment it in order
>> to
>> > create a mesh of the volume. What are the steps to do this and how do I
>> > follow through with each step? I tried to watch the youtube tutorials
>> on the
>> > Freesurfer youtube, but since they are slides informing of what
>> Freesurfer
>> > can do and not quite a play-by-play interaction of Freeview, I am stuck.
>> >
>> > Thanks
>> >
>> > Abbie
>> >
>> > On Mon, Jun 27, 2016 at 3:30 PM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> > wrote:
>> >   Hi Abbie
>> >
>> >   what are you trying to create a mesh of? We supply meshes for
>> >   the
>> >   gray/white interface and for the pial surface. We supply voxel
>> >   segmentations of lots of other things that you could mesh, but
>> >   we don't
>> >   by default.
>> >
>> >   cheers
>> >   Bruce
>> >   On Mon, 27 Jun 2016, Abbie McNulty wrote:
>> >
>> >   > Hello,
>> >   > I am trying to segment a MRI brain in order to create a mesh
>> >   of the image
>> >   > into finite elements, but I am very new with
>> >   Freesurfer/Freeview and am not
>> >   > familiar with the tools. So far, I have only uploaded
>> >   brain.mgt from the
>> >   > bert file that comes with the program. If I wanted to mesh
>> >   this brain, how
>> >   > should I proceed? The online tutorials have confused me
>> >   especially since I
>> >   > am not sure if I am supposed to be using the terminal or the
>> >   command window
>> >   > for a lot of the code commands.
>> >   >
>> >   > Any help would be appreciated.
>> >   >
>> >   > Thanks!
>> >   >
>> >   > Abbie McNulty
>> >   >
>> >   > --
>> >   > Abigail C. McNulty
>> >   > Stanford University Class of 2018
>> >   > B.A. Candidate in Bioengineering
>> >   > Stanford Women's XC/ Track and Field
>> >   >
>> >   >
>> > ___
>> > Freesurfer mailing list
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>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
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>> >
>> >
>> >
>> >
>> > --
>> > Abigail C. McNulty
>> > Stanford University Class of 2018
>> > B.A. Candidate in Bioengineering
>> > Stanford Women's XC/ Track and Field
>> >
>> >
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>>
>
>
>
> --
> Abigail C. McNulty
> Stanford University Class of 2018
> B.A. Candidate in Bioengineering
> Stanford Women's XC/ Track and Field
>



-- 
Abigail C. McNulty
Stanford University Class of 2018
B.A. Candidate in Bioengineering
Stanford Women's XC/ Track and Field
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Re: [Freesurfer] Any updates on recon-all GPU support?

[Derek Pisner]

Hi Richard,

Many thanks for your effort and help. The binaries did not work unfortunately 
seemingly because of libcuda from 6.5 not being forward compatible with libcuda 
from 7.5, as you noted.

-Derek

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of R Edgar 
[freesurfer@gmail.com]
Sent: Sunday, July 03, 2016 3:06 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Any updates on recon-all GPU support?

On 2 July 2016 at 19:06, Derek Pisner  wrote:

> Thanks anyway for taking a look. Despite a number of further tweaks to our 
> cuda libraries, we have made no further progress with this.  Any chance you 
> could pass along your cuda binaries so that I can see whether they might just 
> "work"? Very curious.

I've sent a tarball in a separate email - let me know if it gets
through. I wouldn't be too hopeful, though - I don't know that libcuda
is forward compatible.

Regards,

Richard
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Re: [Freesurfer] TRACULA group stats visualization

[Derek Pisner]

Hi Anastasia,

This occurs for me on both stable and dev versions of freview and trac-all -stat

-Derek

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
[ayend...@nmr.mgh.harvard.edu]
Sent: Monday, July 04, 2016 12:47 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA group stats visualization

Hi Derek - Are you by any chance using the dev version of freeview?

a.y

On Fri, 1 Jul 2016, Derek Pisner wrote:

> Dear Anastasia,
> I am running into an issue with the trac-all -stat option on our longitudinal 
> TRACULA data.
>
> Everything runs smoothly through all earlier stages, and I checked individual 
> subjects' merged outputs in freeview with -tv mode. Everything looks fine.
>
> Also, then when I run trac-all -c dmric_config -stat, everything finishes 
> without error.
>
> But then when I open the results with the command:
> freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w 
> /data/blt/TRACULA/tractography_output/stats.long/*.path.mean.txt
>
> I get the image seen in the attached .png file. Any idea what might be 
> causing this?
>
> Many thanks in advance for you help.
>
> Best,
> Derek
>
>
>
>

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Re: [Freesurfer] trac-all error (bvecs and bvals don't have same number of entries)

[Anastasia Yendiki]

Hi there - I think I know what it is, but it's a problem that should be 
solved if you have the last tracula update. It means that your LANG 
environment variable needs to be set to en_US.UTF-8, which the update does 
for you.


a.y

On Tue, 5 Jul 2016, Lars M. Rimol wrote:



Hi Anastasia,

I have attached the dmri/bvals and dmri/bvec ("bvals"/"bvecs") and the
dmri/dwi_orig.mghdti* files. I don't know if it's a problem but the
generated bvec file has commas instead of full stop (0,832 instead of
0.832). The input file (attached: "bvec_rows") has full stop. Another thing
is that the generated bvals file has an empty space at the end of the row,
which is not there in the input file ("bvals_rows").



thank you!

LMR

Hi Lars - At first glance, these files look fine to me. Do the dmri/bvals
and dmri/bvecs files that get generated look fine too?

a.y

On Sat, 2 Jul 2016, Lars M. Rimol wrote:

Hi,

Trying to run trac-all -c dmric_file -prep,  I get an error message stating 
that there are different numbers of entries in the bval and bvec files. I do

n't
understand why, since both have the same number of rows (64).

OS = Ubuntu 14.04.4
Software: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0; I have updated 
Tracula and FSL (v 5.0.9).



Error message:

#@# Tensor fit fr. 01. juli 19:20:29 +0200 2016
dtifit -k /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dwi.nii.gz -m 
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dlabel/diff/aparc+aseg_mask.bbr.n

ii.gz
 -r
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvecs -b 
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvals -o

/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dtifit
Error: bvecs and bvals don't have the same number of entries
Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 U
TC 
2015 x86_64 x86_64 x86_64 GNU/Linux


trac-preproc exited with ERRORS at fr. 01. juli 19:20:30 +0200 2016

--
I also tried flipping the bvec/bval files, but got the same error.
I don't know if there's anything wrong with the bval/bvec files, or if this 
error message is indicative of some other problem. Is the updated Tracula

version only compatible with the dev version of FS?

I have attached the bval/bvec files and the trac-all.log.

---
The contents of the dmric file is:

setenv SUBJECTS_DIR  /media/lmr2/subjects/DTI
set dtroot =  /media/lmr2/subjects/DTI/tracula_2016_nativerows
set subjlist = (4_FS)
set dcmroot =  /media/lmr2/subjects/DTI
set dcmlist =   ( 4/5/1.dcm )
set bvalfile = /media/lmr2/subjects/DTI/bvals_rows.csv
set bvecfile = /media/lmr2/subjects/DTI/bvec_rows.csv



Thank you!


yours,

Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway










sincerely yours,

Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway




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Re: [Freesurfer] Apply mris_apply_reg for a label

[Douglas N Greve]

I think it will be easier with mris_apply_reg. You might need to get the 
newest version with can handle labels

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_apply_reg

run it something like
mris_apply_reg --src-label lh.source.label --streg lh.sphere.left_right 
rh.sphere.left_right --trg rh.lh.source.label

doug

On 06/17/2016 10:33 AM, Alexandre Routier wrote:
> Hello,
>
> I am a little but confused with the syntax: I have a drawn label 
> lh.manual.label and I want it on the right hemisphere and I was 
> thinking of this command:
> mri_label2label --srcsurfreg lh.sphere.reg --targsurfreg rh.sphere.reg 
> --surfreg lh.sphere.left_right --regmethod surface --hemi lh 
> --srclabel lh.manual.label --targlabel rh.manual.label
>
> (I have the following sphere files for my subject : ?h.qsphere.nofix, 
> ?h.sphere, ?h.sphere.left_right, ?h.sphere.reg)
>
> I don't see how to include ?h.sphere.left_right to the command line.
>
> Alexandre
>
>
> 2016-06-16 18:53 GMT+02:00 Bruce Fischl  >:
>
> Hi Alexandre
>
> try mri_label2label using the ?h.sphere.left_right
>
> cheers
> Bruce
>
> On Thu, 16 Jun 2016, Alexandre Routier wrote:
>
> Hello everyone,
> I have a label for the left hemisphere for my subject but I
> don't understand
> the syntax to apply mris_apply_reg on this label to obtain the
> right
> hemisphere version.
>
> mris_left_right_register was performed to get lh.sphere.left_right
> and lh.sphere.left_right but I don't know how to use this for
> the mris_apply_reg command.
>
> Thanks in advance for your answer.
>
> Alexandre
>
>
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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] FSFAST time series extraction

[Douglas N Greve]

has this question been answered?

On 06/17/2016 09:42 AM, curry_sa...@yahoo.com wrote:
> Hi all,
>
> I am trying to extract mean time series BOLD data using FSFAST from 
> Cortical ROIs + sub cortical ROIs and cerebellum.
>
> preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 
> -fwhm 6 -per-run -stc oddmri_segstats --annot fsaverage lh aparc 
> --i rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz --excludeid 
> 1000 --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt
> mri_segstats --annot fsaverage rh aparc --i 
> rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000 
> --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt
>
> and for cortical time series
>
> mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab 
> /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13 
> --id 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 
> 54 --id 58 --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz 
> --avgwf subCorticalTimeSeries.txt
>
> But I am not sure on how exactly to extract time series from 
> cerebellar regions. So if I want to extract time series from regions 
> as described in Buckner et.al 2011. Could I just use mri_segstats for 
> the labels 601-628 in FreeSurferCololLUT.txt? If not could you please 
> direct me to processes that I can use.
>
>
>
> Sent from Yahoo Mail. Get the ap 
>
>
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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
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Registering scans with different voxel sizes/numbers

[Martin Reuter]

By the way, freesurfer registers all images to the within subject template in the base stream, so they are already  registered for you. The command is mri_robust_template.
Best Martin
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Re: [Freesurfer] Hippocampal Subfields Segmentation

[pierre deman]

Hi,
I still have a problem as well with the subfields segmentation (ubuntu
14.04, with the files .ctf)

Cheers,
Pierre
Hello FreeSurfer Experts,

I’m having issues with the hippocampal subfields segmentation using OS X
Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer  Subject Stamp:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0   Current Stamp:
freesurfer-Linux-centos6_x86_64-dev-20160616-8264611.

I ran the recon-all -s VE002 -hippocampal-subfields-T1 command and keep
getting an error message : Error:CTF file
'/usr/local/freesurfer-dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf'
failed to open for 'Read' access. Error message: 'Open a zip file for
read/modify failed.’

The segmented hippocampal files as described on free surfer wiki cannot be
found under the subject ‘mri’ folder.
I understand other users have complained of a similar issue within the last
week.

I’d ve grateful if you could assist me with the issue above.

Many thanks
Permesh




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Re: [Freesurfer] clarification

[Martin Reuter]

Hi,
Images from different scanners can look very differently (intensity, scaling, non linearities). Also acquisition parameters can change images and bias results. 
This warning exists to make sure users understand that whatever they get out of the analysis could be completely driven by acquisition differences rather than disease/drug effects. 
I don't know exactly what you are asking about FSL, but in freesurfer we conform to 1 mm isotropic. This does not correct or remove any of this acquisition bias, only it makes sure that all components work with the same resolution internally.
Depending on your study design (how many time point in each scanner, test retest on different scanners with short time distance etc) could be that you may not be able to draw any conclusions from your data. We once saw growing brains after a scanner software update. Changing hardware will be a large difference.
Sorry, Martin
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Re: [Freesurfer] Z-stat - z.mgh

[Douglas N Greve]

You can use the version 6 mri_glmfit which you can get from here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit

On 06/16/2016 07:51 AM, Robby De Pauw wrote:
>
> Dear FreeSurfer users
>
> I am not able to extract the Z-values as they are not present in my 
> output:
>
> z.mgh -- z-stat that corresponds to the significance
>
> Are these Z-values always produced (or only in case of two group 
> comparison)? Is there a way to produce this map myself?
>
> This is my output after fitting the model (mri_glmfit) and after 
> clusterwise correction for MC:
>
> C.dat cache.th13.abs.sig.voxel.mgh
>
> F.asc cache.th13.abs.y.ocn.dat
>
> F.csv cnr.mgh
>
> F.mgh gamma.mgh
>
> cache.th13.abs.pdf.dat gammavar.mgh
>
> cache.th13.abs.sig.cluster.mgh maxvox.dat
>
> cache.th13.abs.sig.cluster.summary sig.asc
>
> cache.th13.abs.sig.masked.mgh sig.csv
>
> cache.th13.abs.sig.ocn.annot sig.mgh
>
> cache.th13.abs.sig.ocn.mgh
>
> I am currently working on the latest version of FreeSurfer:
>
> freesurfer-Darwin-lion-stable-pub-v5.3.0
>
> Thank you for your response,
>
> Greetings
>
> Robby
>
> Robby De Pauw, PT, MT, drs.
>
> *T *+32 09 332 12 19* | Email *robby.dep...@ugent.be 
> 
>
> Ghent University *| *Rehabilitation Sciences and Physiotherapy
>
> Campus Heymans 3B3 (022)
>
> De Pintelaan 185 BE-9000 Ghent
>
> Route to my office 
>
>
>
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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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[Freesurfer] retinotopic analysis

[Francesca Strappini]

Hello Freesurfers,

Where can I find any documentation about how is retinotopic analysis
performed in Freesurfer? Thanks.

Best

-- 
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il
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Re: [Freesurfer] Maps/seed on surafce

[Douglas N Greve]

Have you verified that the Anat-Func registration in FreeSurfer is 
correct? You can view it with tkregister-sess.


On 06/16/2016 10:26 AM, Martin Juneja wrote:
> Hi Dr. Greve,
>
> I used following command for this:
>
> mkanalysis-sess -analysis LH_XY.surf.lh 
> -surface fsaverage lh -fwhm 5 -notask -taskreg LH_XYZ.dat 1 -nuisreg vcsf.dat 
> 5 -nuisreg wm.dat 5 
>

>  -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR  3.
>
> Thanks.
>
> On Wed, Jun 15, 2016 at 3:07 PM, Douglas N Greve 
> > wrote:
>
> what was your mkanalysis-sess command?
>
> On 06/08/2016 02:10 PM, Martin Juneja wrote:
> > Dear FreeSurfer and SPM experts,
> >
> > I am trying to calculate functional connectivity maps using
> FreeSurfer
> > pipeline:
> >
> 
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough.
> >
> > After defining a seed region on raw anatomical image, I
> co-registered
> > functional data with anatomical data (as reference) and made
> sure that
> > the seed is at correct place on both anatomical (top left in
> attached
> > image) and functional (top right) data. Using SPM, I confirmed
> > co-registration was fine.
> >
> > But after running all the steps of FC, looks like the FC maps
> are not
> > correct: sig.nii.gz at -fthresh 2 3 (shown at bottom left) because I
> > am not getting significant FC at seed location. Here, bottom right
> > shows the seed location on surface after I convert the seed to
> > fsaverage space (for visualization purpose).
> >
> > Any thoughts, ideas or tips on what went wrong here, would be really
> > appreciated.
> >
> > Thanks.
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> 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
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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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
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> but does not contain patient information, please contact the
> sender and properly
> dispose of the e-mail.
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-- 
Douglas N. Greve, Ph.D.
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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Re: [Freesurfer] convert from MNI152 to native space

[Douglas N Greve]

Try now

On 06/15/2016 06:30 PM, Leila Reddy wrote:
> Hi Doug,
>
> Thanks for your reply.
>
> When I run mni152reg I get an error : ERROR: Flag --lta unrecognized
>
> I'm using v 1.9 of this file.
>
> I found a post that said to download a newer version from here:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mni152reg
>
> but it doesn't seem to be there anymore.
>
> Thanks,
> Leila
>
> On Wednesday, June 15, 2016 11:55 AM, Leila Reddy  wrote:
>
>
> Hi,
>
> I have a binary mask from the WFU_Pickatlas. I think this mask in in 
> the MNI152 space (when I load_nifti in Matlab I get dimensions of [91 
> 109 91]. I would like to convert this mask into the native space of 
> each subject. I tried the following command but the results do not 
> look right in Freeview:
>
>  mri_vol2vol --mov mask_MNI152.nii --targ bold/005/f.nii.gz --o 
> mask_in_Native.nii --mni152reg
>
> The overlay of the mask on f.nii in Freeview is mostly outside the brain.
>
> How can I go about this step?
>
> Thanks for your help,
> Leila
>
>
>
>
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-- 
Douglas N. Greve, Ph.D.
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
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] clarification

[zalewk]

My apologies as I misstated some of the data in my first email,

The voxel sizes are relatively similar, (two of the acquisitions are 1mm vs one 
with 0.9mm). 
Whereas the FOV is different between the scans being 256x256x176 on one 
acquisition, 224x256x176 on the second and 240x240x180 on the third.

KZ

On Tue, 5 Jul 2016, zal...@u.washington.edu wrote:

> Hello Freesurfer team,
>
> I have the unfortunate task of performing longitudinal volumetric analysis on 
> subjects collected on three different scanners with different voxel 
> numbers/sizes. I didn't find this out until attempting to run the 
> longitudinal base and receiving this message:
>
> WARNING: Image geometries differ across time, maybe due to aquisition changes?
> This can potentially bias a longitudinal study! Will continue in 10s.
>
> By re-registering the original nifti and recreating the norm.mgz/talairach I 
> can correct the geometry, but FSL's Flirt will only work with niftis and not 
> mgz volumes, ergo I can't re-register the manually edited brainmask/wm 
> volumes properly.
> I was wondering if there were any freesurfer tools I could use to simply 
> re-register the .mgz volumes to the new norm.mgz? If so, how would I go about 
> doing that? Seeing as the brainmask/wm are both registered to 256^3/1mm 
> anyhow, is this something I should even be concerned about?
>
> Thanks,
> KZ
>
>
>

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[Freesurfer] Registering scans with different voxel sizes/numbers

[zalewk]

Hello Freesurfer team,
 
I have the unfortunate task of performing longitudinal volumetric analysis on 
subjects collected on three different scanners with different voxel 
numbers/sizes. I didn't find this out until attempting to run the longitudinal 
base and receiving this message:
 
WARNING: Image geometries differ across time, maybe due to aquisition changes?
 This can potentially bias a longitudinal study! Will continue in 10s.

By re-registering the original nifti and recreating the norm.mgz/talairach I 
can correct the geometry, but FSL's Flirt will only work with niftis and not 
mgz volumes, ergo I can't re-register the manually edited brainmask/wm volumes 
properly. 
I was wondering if there were any freesurfer tools I could use to simply 
re-register the .mgz volumes to the new norm.mgz? If so, how would I go about 
doing that? Seeing as the brainmask/wm are both registered to 256^3/1mm anyhow, 
is this something I should even be concerned about?  

Thanks, 
KZ


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[Freesurfer] Hippocampus & Amygdala Volume Accuracy

[Limachia, Gaurang (NIH/NINDS) [F]]

Hello Bruce,

I am uploading the data set to filedrop for you to look over. Can you assist us 
in determining the optimal method for parcellation of the white and gray 
matter. We are particularly interested in determining the volume of the 
hippocampus and amygdala. Are there any special parameters we should use for 
these structures? Therefore, we want to improve the accuracy of the pial and 
white matter surfaces. I would greatly appreciate your help.

Best Regards,

Shyam
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[Freesurfer] retinotopy analysis documentation

[Francesca Strappini]

Hello Freesurfers,

I'm re-posting this question. Where can I find any documentation about how
is the retinotopic analysis performed in Freesurfer? Thanks.

Best

-- 
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il
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Re: [Freesurfer] Order of overlays

[dgw]

You can also do this now, by simply changing the alpha level of the
colors in the CLUT, (note this only works in the dev version).

hth
d

On Sat, Jul 2, 2016 at 1:46 PM, Douglas Greve  wrote:
> Yes, you can. If I remember correctly, you can goto view->configure overlay,
> then find the item to specify that you want the labels under the activation.
>
>
> On 6/29/16 5:22 AM, Reza Rajimehr wrote:
>
> Hi,
>
> In Tksurfer, we want to show functional activity map and borders of aparc on
> a surface. The borders of aparc are always drawn on top of the activity map,
> which sometimes hide small activation blobs. Is it possible to draw the
> activity map on top of the aparc borders?
>
> Reza
>
>
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>
>
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>
>
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> 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
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Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

[Douglas N Greve]

can you answer the question that it asks?

On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:
> Hi everyone,
>
> I’m having some issues converting my DICOMs (DWI) into NIFTI using 
> mri_convert. I looked for other topics with people having the same 
> kind of problem but couldn’t find an answer.
>
> Each time I run mri_convert on my DICOMs I get the following error :
> WARNING: file MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 
> does not contain a Siemens ASCII header
> has this file been anonymized?
> ERROR: cannot unpack mosiacs without ASCII header
>
> Here are the following DICOMs informations :
> Identification
> NumarisVer   syngo MR D13
> ScannerModel Skyra
> PatientName   x
> Date and time
> StudyDate 20140918
> StudyTime 121037.203000
> SeriesTime   123450.60
> AcqTime   123257.367500
> Acquisition parameters
> PulseSeq ep_b0
> Protocol AX DTI no angle MS NEX 4 2
> PhEncDir COL
> EchoNo   1
> FlipAngle 90
> EchoTime 96
> InversionTime -1
> RepetitionTime   4700
> PhEncFOV 0
> ReadoutFOV   0
> Image information
> RunNo 4
> SeriesNo 5
> ImageNo   1
> NImageRows   990
> NImageCols   990
> NFrames   64
> SliceArraylSize   0
> IsMosaic 1
> ImgPos   1075.1575 1069.8385 -48.6769
> VolRes 2.1818   2.1818   2.
> VolDim 000
> Vc -1.  -0.   0.
> Vr -0.  -1.   0.
> Vs 0.   0.   0.
> VolCenter   0.   0.   0.
> TransferSyntaxUID 1.2.840.10008.1.2.1
>
>
> Then I try using mri_convert -it dicom, it converts the files but not 
> as it is expected, you could notice the difference when I run mri_info 
> on my output :
> Volume information for output.nii.gz
>   type: nii
> dimensions: 990 x 990 x 1 x 64
>voxel sizes: 2.1818, 2.1818, 2.
>   type: SHORT (4)
>fov: 2160.000
>dof: 0
> xstart: -1080.0, xend: 1080.0
> ystart: -1080.0, yend: 1080.0
> zstart: -1.0, zend: 1.0
> TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip 
> angle: 0.00 degrees
>nframes: 64
>PhEncDir: UNKNOWN
> ras xform present
> xform info: x_r =  -1., y_r =  -0., z_r = -0., c_r =  
>   -4.8425
>   : x_a =  -0., y_a =  -1., z_a = -0., c_a =   
> -10.1615
>   : x_s =   0., y_s =   0., z_s = 1., c_s =   
> -47.6769
> Orientation   : LPS
> Primary Slice Direction: axial
>
> voxel to ras transform:
>-2.1818  -0.  -0.  1075.1575
>-0.  -2.1818  -0.  1069.8385
> 0.   0.   2.   -48.6769
> 0.   0.   0. 1.
>
> voxel-to-ras determinant 9.52066
>
> ras to voxel transform:
>-0.4583   0.   0.   492.7805
> 0.  -0.4583   0.   490.3426
>-0.  -0.   0.500024.3384
> 0.   0.   0. 1.
>
> I would really appreciate your help, thank you.
>
> Best,
>
> Ismail
>
>
>
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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
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

[Koubiyr, Ismail]

The file has not been anonymized.

Thanks,

Ismail 

> On Jul 5, 2016, at 11:20 AM, Douglas N Greve  
> wrote:
> 
> can you answer the question that it asks?
> 
> On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:
>> Hi everyone,
>> 
>> I’m having some issues converting my DICOMs (DWI) into NIFTI using 
>> mri_convert. I looked for other topics with people having the same 
>> kind of problem but couldn’t find an answer.
>> 
>> Each time I run mri_convert on my DICOMs I get the following error :
>> WARNING: file MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 
>> does not contain a Siemens ASCII header
>> has this file been anonymized?
>> ERROR: cannot unpack mosiacs without ASCII header
>> 
>> Here are the following DICOMs informations :
>> Identification
>> NumarisVer   syngo MR D13
>> ScannerModel Skyra
>> PatientName   x
>> Date and time
>> StudyDate 20140918
>> StudyTime 121037.203000
>> SeriesTime   123450.60
>> AcqTime   123257.367500
>> Acquisition parameters
>> PulseSeq ep_b0
>> Protocol AX DTI no angle MS NEX 4 2
>> PhEncDir COL
>> EchoNo   1
>> FlipAngle 90
>> EchoTime 96
>> InversionTime -1
>> RepetitionTime   4700
>> PhEncFOV 0
>> ReadoutFOV   0
>> Image information
>> RunNo 4
>> SeriesNo 5
>> ImageNo   1
>> NImageRows   990
>> NImageCols   990
>> NFrames   64
>> SliceArraylSize   0
>> IsMosaic 1
>> ImgPos   1075.1575 1069.8385 -48.6769
>> VolRes 2.1818   2.1818   2.
>> VolDim 000
>> Vc -1.  -0.   0.
>> Vr -0.  -1.   0.
>> Vs 0.   0.   0.
>> VolCenter   0.   0.   0.
>> TransferSyntaxUID 1.2.840.10008.1.2.1
>> 
>> 
>> Then I try using mri_convert -it dicom, it converts the files but not 
>> as it is expected, you could notice the difference when I run mri_info 
>> on my output :
>> Volume information for output.nii.gz
>>  type: nii
>>dimensions: 990 x 990 x 1 x 64
>>   voxel sizes: 2.1818, 2.1818, 2.
>>  type: SHORT (4)
>>   fov: 2160.000
>>   dof: 0
>>xstart: -1080.0, xend: 1080.0
>>ystart: -1080.0, yend: 1080.0
>>zstart: -1.0, zend: 1.0
>>TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip 
>> angle: 0.00 degrees
>>   nframes: 64
>>   PhEncDir: UNKNOWN
>> ras xform present
>>xform info: x_r =  -1., y_r =  -0., z_r = -0., c_r =  
>>  -4.8425
>>  : x_a =  -0., y_a =  -1., z_a = -0., c_a =   
>> -10.1615
>>  : x_s =   0., y_s =   0., z_s = 1., c_s =   
>> -47.6769
>> Orientation   : LPS
>> Primary Slice Direction: axial
>> 
>> voxel to ras transform:
>>   -2.1818  -0.  -0.  1075.1575
>>   -0.  -2.1818  -0.  1069.8385
>>0.   0.   2.   -48.6769
>>0.   0.   0. 1.
>> 
>> voxel-to-ras determinant 9.52066
>> 
>> ras to voxel transform:
>>   -0.4583   0.   0.   492.7805
>>0.  -0.4583   0.   490.3426
>>   -0.  -0.   0.500024.3384
>>0.   0.   0. 1.
>> 
>> I would really appreciate your help, thank you.
>> 
>> Best,
>> 
>> Ismail
>> 
>> 
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
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[Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

[Koubiyr, Ismail]

Hi everyone,

I’m having some issues converting my DICOMs (DWI) into NIFTI using mri_convert. 
I looked for other topics with people having the same kind of problem but 
couldn’t find an answer.

Each time I run mri_convert on my DICOMs I get the following error :
WARNING: file MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 does not 
contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header

Here are the following DICOMs informations :
Identification
NumarisVersyngo MR D13
ScannerModel  Skyra
PatientName   x
Date and time
StudyDate 20140918
StudyTime 121037.203000
SeriesTime123450.60
AcqTime   123257.367500
Acquisition parameters
PulseSeq  ep_b0
Protocol  AX DTI no angle MS NEX 4 2
PhEncDir  COL
EchoNo1
FlipAngle 90
EchoTime  96
InversionTime -1
RepetitionTime4700
PhEncFOV  0
ReadoutFOV0
Image information
RunNo 4
SeriesNo  5
ImageNo   1
NImageRows990
NImageCols990
NFrames   64
SliceArraylSize   0
IsMosaic  1
ImgPos1075.1575 1069.8385 -48.6769
VolRes  2.1818   2.1818   2.
VolDim  000
Vc -1.  -0.   0.
Vr -0.  -1.   0.
Vs  0.   0.   0.
VolCenter   0.   0.   0.
TransferSyntaxUID 1.2.840.10008.1.2.1


Then I try using mri_convert -it dicom, it converts the files but not as it is 
expected, you could notice the difference when I run mri_info on my output :
Volume information for output.nii.gz
  type: nii
dimensions: 990 x 990 x 1 x 64
   voxel sizes: 2.1818, 2.1818, 2.
  type: SHORT (4)
   fov: 2160.000
   dof: 0
xstart: -1080.0, xend: 1080.0
ystart: -1080.0, yend: 1080.0
zstart: -1.0, zend: 1.0
TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
   nframes: 64
   PhEncDir: UNKNOWN
ras xform present
xform info: x_r =  -1., y_r =  -0., z_r =  -0., c_r =-4.8425
  : x_a =  -0., y_a =  -1., z_a =  -0., c_a =   -10.1615
  : x_s =   0., y_s =   0., z_s =   1., c_s =   -47.6769
Orientation   : LPS
Primary Slice Direction: axial

voxel to ras transform:
   -2.1818  -0.  -0.  1075.1575
   -0.  -2.1818  -0.  1069.8385
0.   0.   2.   -48.6769
0.   0.   0. 1.

voxel-to-ras determinant 9.52066

ras to voxel transform:
   -0.4583   0.   0.   492.7805
0.  -0.4583   0.   490.3426
   -0.  -0.   0.500024.3384
0.   0.   0. 1.

I would really appreciate your help, thank you.

Best,

Ismail

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[Freesurfer] Hippocampal Subfields Segmentation

[Permesh Dhillon]

Hello FreeSurfer Experts,

I’m having issues with the hippocampal subfields segmentation using OS X 
Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer  Subject Stamp: 
freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0   Current Stamp: 
freesurfer-Linux-centos6_x86_64-dev-20160616-8264611.

I ran the recon-all -s VE002 -hippocampal-subfields-T1 command and keep getting 
an error message : Error:CTF file 
'/usr/local/freesurfer-dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf' 
failed to open for 'Read' access. Error message: 'Open a zip file for 
read/modify failed.’

The segmented hippocampal files as described on free surfer wiki cannot be 
found under the subject ‘mri’ folder.
I understand other users have complained of a similar issue within the last 
week.

I’d ve grateful if you could assist me with the issue above.

Many thanks
Permesh




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Re: [Freesurfer] trac-all error (bvecs and bvals don't have same number of entries)

[Lars M. Rimol]

Hi Anastasia,

I have attached the dmri/bvals and dmri/bvec ("bvals"/"bvecs") and the
dmri/dwi_orig.mghdti* files. I don't know if it's a problem but the
generated bvec file has commas instead of full stop (0,832 instead of
0.832). The input file (attached: "bvec_rows") has full stop. Another thing
is that the generated bvals file has an empty space at the end of the row,
which is not there in the input file ("bvals_rows").



thank you!

LMR

Hi Lars - At first glance, these files look fine to me. Do the dmri/bvals and
dmri/bvecs files that get generated look fine too?

a.y

On Sat, 2 Jul 2016, Lars M. Rimol wrote:


Hi,

Trying to run trac-all -c dmric_file -prep,  I get an error message stating
that there are different numbers of entries in the bval and bvec files. I don't
understand why, since both have the same number of rows (64).

OS = Ubuntu 14.04.4
Software: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0; I have updated
Tracula and FSL (v 5.0.9).


Error message:

#@# Tensor fit fr. 01. juli 19:20:29 +0200 2016
dtifit -k /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dwi.nii.gz -m
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
 -r
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvecs -b
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvals -o
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dtifit
Error: bvecs and bvals don't have the same number of entries
Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 UTC
2015 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at fr. 01. juli 19:20:30 +0200 2016

--
I also tried flipping the bvec/bval files, but got the same error.
I don't know if there's anything wrong with the bval/bvec files, or if this
error message is indicative of some other problem. Is the updated Tracula
version only compatible with the dev version of FS?

I have attached the bval/bvec files and the trac-all.log.

---
The contents of the dmric file is:

setenv SUBJECTS_DIR  /media/lmr2/subjects/DTI
set dtroot =  /media/lmr2/subjects/DTI/tracula_2016_nativerows
set subjlist = (4_FS)
set dcmroot =  /media/lmr2/subjects/DTI
set dcmlist =   ( 4/5/1.dcm )
set bvalfile = /media/lmr2/subjects/DTI/bvals_rows.csv
set bvecfile = /media/lmr2/subjects/DTI/bvec_rows.csv



Thank you!


yours,

Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway











sincerely yours,

Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway


bvals_rows
Description: Binary data


bvec_rows
Description: Binary data


bvals
Description: Binary data


bvecs
Description: Binary data


dwi_orig.mghdti.bvals
Description: Binary data


dwi_orig.mghdti.bvecs
Description: Binary data
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Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

[Anastasia Yendiki]

You get the same error as trac-all because trac-all runs mri_convert. I'd 
send the mri_convert error in a new email with mri_convert somewhere in 
the title, so that someone else can help you.


On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:


Also when I run mir_convert on the DICOMs I get the same error as the one I
got when I used DICOMs :
WARNING: 
file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/3T2/MR.1.3.12.2.1107.5.2.19.
45306.2014091812330393354083931 does not contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header

Any idea what this could be ?

Thanks,

Ismail

  On Jul 4, 2016, at 3:15 PM, Koubiyr, Ismail
   wrote:

It says 1 … I don’t understand why I get that knowing that when I open
the nifti I can go through the frames …

Ismail

  On Jul 4, 2016, at 3:11 PM, Anastasia Yendiki
   wrote:


  I do not know why the dicoms do not work. When you run
  mri_info on your nifti, what is the number of frames that
  shows up?

  On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:

Hi Anastasia,

This is what’s weird, my nifti volume contains
64 frames as my bvecs/bvals. So this shouldn’t
be the reason.
Also why the DICOMs wouldn’t work at the
beginning ?

Thanks,
Ismail

  On Jul 4, 2016, at 2:41 PM,
  Anastasia Yendiki
  
  wrote:


  Hi Ismail - You can see from the
  log file that the command that
  causes the error is this:

  mri_convert --frame 31
  
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz
  
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz

  It's trying to extract the 32nd
  frame of your nifti file, but from
  the error message it looks like
  your nifti file doesn't have a
  32nd frame. So either the nifti
  file has too few volumes, or the
  bvecs/bvals have too many lines.
  You'll have to figure that out.

  a.y

  On Mon, 4 Jul 2016, Koubiyr,
  Ismail wrote:

Hi Anastasia,
Here it is.
But how could the
problem be related to
the nifti volume since
I have errors
when using the DICOMs
too ?
Thanks again,
Ismail
  On Jul 4,
  2016, at
  1:44 PM,
  Anastasia
  Yendiki


wrote:


  Hi Ismail
  - It
  sounds
  like the
  error has
  to do with
  the nifti
  volume,
  not

the bvecs/bvals. Can
you send the log file
from
scripts/trac-all.log?

  Thanks,
  a.y

  On Mon, 4
  Jul 2016,
  Koubiyr,
  Ismail
  wrote:

Hi
Anastasia,
Thank
you
for
getting
back
to
me.
Here
are
more
details
about
my
problem,
I
think
it
should
help
you
understand
more.
I
run