Re: [Freesurfer] Extracting BOLD from a flattened surface

[Taha Abdullah]

Hello Freesurfer Team,

Sorry for being so late with this message I was trying different things to
accomplish extracting BOLD values from a flattened surface. I followed the
overall instructions on this website
http://web.mit.edu/fsl_v5.0.8/fsl/doc/wiki/FreeSurfer.html. I have the
flattened patch from tksurfer and I want to conduct a rsfMRI analysis on a
flattened patch from a feat directory. Do you have any recommendations on
the proper workflow? I believe that I need to run

mri_label2vol --annot /path to subj/label/lh.aparc.annot --temp
func4d.nii.gz --reg (output from reg-feat2anat) --o myoutput --hemi lh
--subject --proj 0 1 .1

The output has similar dimensions as functional and it is only cortical
areas but the time dimensions are no longer there. Not sure how to actually
extract the bold signal, maybe something with mri_segstats? And I think it
will be straightforward to understand the spatial changes occurring during
flattening since vertex identity stays the same and can be read in MATLAB,
correct? Please let me know at your earliest convenience.

Best,
Taha

On Thu, May 5, 2016 at 9:21 AM, Douglas Greve 
wrote:

> So you have 1 column, but you want 1 column for each vertex? We don't have
> anything to do that, but you can do it in matlab, eg,
> M = fast_vol2mat(MRIread('lh.yourdata.mgh'));
> M will be a 240x127000 matrix
>
>
> On 5/4/16 8:36 PM, Taha Abdullah wrote:
>
> Hello Doug,
>
> Sorry for the confusing and long email, I am interested in extracting the
> raw BOLD signal from a processed 4D nifit file. After registering the
> functional to ${subject}/mri/orig.mgz and generating the registration file,
> I proceeded to convert the functional image to the same dimensions as
> the lh.inflated surface via mri_vol2surf so the functional data image now
> has 127000 x 1 x 1 x 240. So I ran mri_segstats command to extract the bold
> signal, but I ended up having 240 rows and 1 column in the text file...the
> ultimate goal is to quantify the wave propagation of the BOLD time series
> across a flattened patch. Any advice would be greatly appreciated.
>
> Thanks!
>
> On Wed, May 4, 2016 at 2:26 PM, Douglas N Greve  > wrote:
>
>>
>> Sorry, can you tell me what you are trying to do? You just want a number
>> of time points -by- number of vertices file? Then mri_vol2surf should do
>> that for you. Flattening is irrelevant for this as it only changes the
>> xyz coordinate of the vertex and not the vertex identity.
>> doug
>>
>>
>> On 04/29/2016 11:24 AM, Taha Abdullah wrote:
>> > Hello Freesurfer Experts,
>> >
>> > Long story short--I would like to extract BOLD values from each TR
>> > across all vertices for one subjects flattened surface
>> > Following is a brief overview of my steps and at the end you can see
>> > where I am stuck.
>> > First, after */recon-all /I* followed the steps to cut the lh inflated
>> > surface, saved as a patch, ran /*mris_flatten, */converted patch into
>> > asc file.
>> > Second, I used read_patch.m to extract all spatial information and a
>> > net loss of approximately 10k vertices (127k to 116k)
>> >
>> > We had all functional images processed in FSL, the 4D file has
>> > 64x64x36x240 dimensions (voxels are 3.4x3.4x3.0). Next, co-registered
>> > the functional and anatomicals together via the following cmd:
>> > */ bbregister --s cbp001_v1 --mov filtered_func_data.nii.gz --bold
>> > --init-fsl --reg dummy1.da/*t. Afterwards, converted the volume to a
>> > surface using the following cmd*/: mri_vol2surf --mov
>> > filtered_func_data.nii.gz --reg dummy1.dat --projfrac 0.5 --interp
>> > trilinear --hemi lh --o ./lh.func.vol2surf.mgh. /*THe dimensions are
>> > 127027 x 1 x 1 x 240. Visually no problem when using*/ tksurfer
>> > cbp001_v1 lh inflated -patch /path to flattened patch/ -overlay
>> > /lh.func.vol2surf.mgh/  -timecourse lh.func.vol2surf.mgh;/* click on
>> > the patch and shows the timecourse for that selected vertex. Using the
>> > View>Configure>overlay I can shuffle through the TRs to inspect the
>> > change in raw BOLD signal per vertex.
>> >
>> > I have been perusing the email web server searching for how to extract
>> > the hemodynamic waveform for each vertex across the flattened surface
>> > and ultimately will be using matlab to understand how the spatial
>> > transformation is happening. As well I have all the matlab files that
>> > seemed relevant to my query (read_surf.m, read_patch.m, and
>> > readMRI.m). I was hoping that I would be able to have a text file with
>> > all the vertices (127K not the flattened 116k) in rows and each column
>> > would have the TRs; I ran this command;*/ mri_segstats --slabel
>> > cbp001_v1 lh
>> > /home/share/freesurfer/subjects/cbp001_v1/label/lh.cortex.label
>> > --avgwf mri_seg_stats.dat --i lh.func.vol2surf.mgh/*, output was the
>> > 240 TRs as rows and seems like the average global BOLD signal in the
>> > single column corresponding with each TR. Excuse my 

Re: [Freesurfer] Mult-Shell Tracula Help

[Anastasia Yendiki]

Hi Kristina - You can enter nifti DWI volumes in the configuration file 
(or any other format that mri_convert can recognize). You should do the 
entire processing from scratch (including bedpost) using the concatenated 
data.

Best,
a.y

On Fri, 20 May 2016, Kristina Jelinkova wrote:

> Hi Anastasia,
>
> Thank you for your response. Yes, we have created the concatenated DWIs and 
> bvec/bval files that we have gotten after running each of the sequences 
> separately from trac-all. How can we run these concatenated nii.gz mages 
> through the ball-and-stick model fit (I'm assuming the configuration file 
> only looks for dcm images)? Would we also need to run bedpostX again 
> separately with the concatenated images?
>
> Thanks again for your help!
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Anastasia Yendiki 
> 
> Sent: Friday, May 20, 2016 3:52:02 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Mult-Shell Tracula Help
>
> Hi Kristina - I'm assuming the 2 data sets were acquired in the same
> session and with the same acquisition parameters, other than the b-values?
> Then you can just concatenate the DWIs from the 2 runs (e.g. with
> mri_concat) and also concatenate the b-value and gradient vector tables
> (and make sure the 2 runs are concatenated in the same order for each type
> of file!)
>
> Best,
> a.y
>
> On Fri, 20 May 2016, Kristina Jelinkova wrote:
>
>>
>> Hello all,
>>
>>
>> I had a question regarding the program Tracula. I have two different DTI 
>> sequences that I wish to run (b=900 and b=2000) but am unsure at which step I
>> am suppose to merge the two sequences together.
>>
>>
>> At this point, I have pre-processed each of the sequences separately using 
>> trac-all. Should I take each of the separate trac-all output
>> data.nii.gz files, merge them, run bedpostX, and then run the ball-and-stick 
>> model fit on the new bedpostX output? Also, is there a way  to use nii.gz
>> files in the configuration file rather than a dcm list?
>>
>>
>> Thank you in advance for your help!
>>
>>
>>
>
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>
>
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Re: [Freesurfer] Mult-Shell Tracula Help

[Kristina Jelinkova]

Hi Anastasia,

Thank you for your response. Yes, we have created the concatenated DWIs and 
bvec/bval files that we have gotten after running each of the sequences 
separately from trac-all. How can we run these concatenated nii.gz mages 
through the ball-and-stick model fit (I'm assuming the configuration file only 
looks for dcm images)? Would we also need to run bedpostX again separately with 
the concatenated images?

Thanks again for your help!

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Anastasia Yendiki 

Sent: Friday, May 20, 2016 3:52:02 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Mult-Shell Tracula Help

Hi Kristina - I'm assuming the 2 data sets were acquired in the same
session and with the same acquisition parameters, other than the b-values?
Then you can just concatenate the DWIs from the 2 runs (e.g. with
mri_concat) and also concatenate the b-value and gradient vector tables
(and make sure the 2 runs are concatenated in the same order for each type
of file!)

Best,
a.y

On Fri, 20 May 2016, Kristina Jelinkova wrote:

>
> Hello all,
>
>
> I had a question regarding the program Tracula. I have two different DTI 
> sequences that I wish to run (b=900 and b=2000) but am unsure at which step I
> am suppose to merge the two sequences together.
>
>
> At this point, I have pre-processed each of the sequences separately using 
> trac-all. Should I take each of the separate trac-all output
> data.nii.gz files, merge them, run bedpostX, and then run the ball-and-stick 
> model fit on the new bedpostX output? Also, is there a way  to use nii.gz
> files in the configuration file rather than a dcm list?
>
>
> Thank you in advance for your help!
>
>
>

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Re: [Freesurfer] Mult-Shell Tracula Help

[Anastasia Yendiki]

Hi Kristina - I'm assuming the 2 data sets were acquired in the same 
session and with the same acquisition parameters, other than the b-values? 
Then you can just concatenate the DWIs from the 2 runs (e.g. with 
mri_concat) and also concatenate the b-value and gradient vector tables 
(and make sure the 2 runs are concatenated in the same order for each type 
of file!)


Best,
a.y

On Fri, 20 May 2016, Kristina Jelinkova wrote:



Hello all, 


I had a question regarding the program Tracula. I have two different DTI 
sequences that I wish to run (b=900 and b=2000) but am unsure at which step I
am suppose to merge the two sequences together. 


At this point, I have pre-processed each of the sequences separately using 
trac-all. Should I take each of the separate trac-all output
data.nii.gz files, merge them, run bedpostX, and then run the ball-and-stick 
model fit on the new bedpostX output? Also, is there a way  to use nii.gz
files in the configuration file rather than a dcm list?


Thank you in advance for your help! 


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[Freesurfer] ERROR: dimension mismatch between input volume and seg

[Kari Parsons]

Hi,

 I'm trying to get some cortical thickness volumes for an ROI that I have 
(I'm pretty much following the instructions at 
https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness verbatim), 
but for some of my subjects I'm getting errors that look like this when I run 
mdi_segstats:

ERROR: dimension mismatch between input volume and seg
  input 1 1 145283
  seg   145283 1 1

 Does anyone have any thoughts on how to trouble-shoot this one?

Thanks!
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Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anastasia Yendiki]

Hi Anri - The FA values are extracted in the native space of each subject, 
which is why those are the only coordinates that you see. If you want to 
display the results of your analysis on an average path, after running 
trac-all -stat, you can use the stats/*.path.mean.txt files (see also the 
last part of the TRACULA tutorial).


Best,
a.y

On Wed, 18 May 2016, Anri WATANABE wrote:


Dear experts, 
I use TRACULA to examine a measure (FA) at each voxel in one pathway.
pathstats.byvoxel.txt files show coordinates in native space and after 
converting those the new files don't show any coordinates which are in MNI 
space.
Could you tell me how can I know MNI coordinate values?

Thank you!


Regards, 
Anri



**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

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Re: [Freesurfer] trac-all problem

[Anastasia Yendiki]

Hi Qi - Is /Studies/*/DTI/dmrirc_subject a single file or multiple files? 
What are the contents of that file?


a.y

On Fri, 6 May 2016, Zeng, Qi wrote:



Hi, 

I am running dti data with trac-all. I followed the command:

trac-all -prep -c /Studies/*/DTI/dmrirc_subject

but it exited with error "Note: indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for 
that dimension." 


Before. there is another post about similar problem

https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/027802.html

Dr. Yendiki suggested it could be because missing defined B0 in the dmrirc, but 
new version wouldn't need this (5.3, a new version?). If so, where can I
 obtain the B0 data? Can I compute from DICOM like nifti and bval, bvec?

Best, 

Qi 


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Re: [Freesurfer] Fwd: trac-all -path error

[Anastasia Yendiki]

Hi Elijah - Since the error occurs in the CST, is any of the brainstem cut 
off for this subject? It's hard to tell from the screenshot, but the field 
of view seems a bit cropped inferiorly.

Best,
a.y

On Thu, 5 May 2016, Elijah Mak wrote:

> Dear Anastasia Yendiki,
> I ran into a hitch while running trac-all -path and came across an identical 
> problem where there was a segmentation fault. I have attached my error and
> log files.
> 
> Loading initial proposal SD's from 
> /subject/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt
> 
> Processing pathway 2 of 18...
> 
> Initializing MCMC
> 
> I have also checked the aparc+aseg and aparc+aseg_mask (overlaid on FA; 
> screenshot attached) as you have suggested, but I can't seem to find anything
> that would have compromised the -path process.
> 
> What else could have gone wrong? trac-all -path works for other subjects.
> 
> Thanks for your help.
> 
> Best Wishes,
> Elijah
> 
> 
> 
>
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Re: [Freesurfer] Inquiry a single curve problem for Tracula outputs

[Anastasia Yendiki]

Hi Xiaofu - It's hard to tell but it looks like the brain mask (which 
comes from the structural data) is a bit too large in the temporal lobe, 
so it's possible that the structural-to-diffusion registration didn't go 
so well for this subject. You can check on this by overlaying the 
structural segmentation transformed into diffusion space (from 
dlabel/diff/aparc+aseg...) onto the FA map.


Best,
a.y

On Sun, 1 May 2016, Xiaofu wrote:


Dear Anastasia or Tracula-group,
   I have run Tracula and found there was only one single curve for some 
tracts. But others went well. I tried setting reinit parameter to 1 and
rerunning
"trac-all -prior" and "trac-all -path" but didn't get improved, e.g., the right 
UNC was a single curve (see attached). I also checked the two end point
set of right UNC (i.e.,endpt1.pd.nii.gz and endpt2.pd.nii.gz) (see attached) 
and found those end points were visually not correct when loaded to FA
image. I guess that may be the reason of the single curve problem. Is there 
anyway to fix this problem? Moreover, do you have any suggestions on the
tract statistics for those single curve tracts. I'd appreciate it if could take 
a look at it for me. If you need more files for the diagnosis please let
me know. 
  Looking forward to hearing from you. Thank you very much.

Best,
Xiaofu

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Re: [Freesurfer] Tracula Pathway reconstruction

[Anastasia Yendiki]

Hi Peggy - If it looks like a single path, it definitely is an 
initialization error. If you reinitialize repeatedly and it doesn't get 
fixed, it might be that something went wrong earlier in the processing 
(for example some part of brain that the tract goes through is missing 
from the brain mask).


Best,
a.y

On Mon, 25 Apr 2016, Peggy Skelly wrote:


Hi Tracula Experts,
How do you determine if a pathway reconstructed well? I've been examining the merged 
pathways (/dpath/merged_avg33_mni_bbr.mgz) in freeview, and
if the pathway looked too small when viewing with the default threshold, I 
would reinitialize those pathways. Most of the time, the new pathway would
look ok upon re-inspection. A few pathways, however, still appear too small 
when viewed at the default threshold in Freeview, but at lower thresholds,
they begin to look ok. 

I've encountered 1 pathway that still appears too small in Freeview, but the 
output in pathstats.overall.txt and pathstats.byvoxel.txt seem reasonable.
On the other hand, its path distribution (path.pd.nii.gz) does not look like a 
distribution, but a single path -- there are a 38 voxels with values of
4000, and all others are 0. This doesn't seem right. What could cause this to 
happen?

What objective measure can I use to determine if a pathway is reconstructed 
well enough?

Thanks,
Peggy

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Re: [Freesurfer] bvals bvecs Error

[Anastasia Yendiki]

Hi Marissa - If your bvecs/bvals files are in row format, you need to make 
sure that you have the most recent update that supports this. It was a 
feature that was added later on:


http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

Best,
a.y

On Fri, 15 Apr 2016, Marissa Pifer wrote:


Hi freesurfers,
I'm having a problem the bvals and bvecs for one of my subject's DTI data. When 
I try to run the first step of tracula I get this error message:

"Error: data and bvals/bvecs do not contain the same number of entries"

I have checked, the bvals and bvecs do contain the same amount of entries (42), 
and they are in the proper format (bvals one line, bvecs three lines).
The entries in the bvals/bvecs matches the number of images within the DTI file 
as well. Looking online, I saw that this was part of the FAQs on
tracula. It suggested making sure the locale settings were correct, which it is 
(en_US.UTF-8). 

I've run tracula on every other subject and have not run into this problem, but 
the same subject had an error with multiple frames when we were
processing the T2 images. Could this be related? Any idea about what is going 
on, or how I can fix it?

Thanks in advance,

Marissa

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Re: [Freesurfer] REPOST: TRACULA dev version: Error message

[Anastasia Yendiki]

Hi Elijah - Are the bvec/bval files located in the current directory from 
where you are running trac-all? This is where it seems to be looking for 
them:


cp 16084.bvec 
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.mghdti.bvecs
cp 16084.bval 
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.mghdti.bvals

If they're in a different location, you need to specify the full path to 
that location, as shown in the sample configuration file.


Best,
a.y

On Fri, 15 Apr 2016, Elijah Mak wrote:


Hi Freesurfer,
Sorry about reposting this email from earlier:

I can't seem to get the TRACULA in the dev version of FS6 to run. 

mv -f 
/Users/MacPro/Documents/NIMROD_DTI/SUBJECT/dmri/dwi_orig_flip.mghdti.bvecs 
/Users/MacPro/Documents/NIMROD_DTI/SUBJECT/dmri/bvecs

mv: rename 
/Users/MacPro/Documents/NIMROD_DTI/SUBJECT/dmri/dwi_orig_flip.mghdti.bvecs to 
/Users/MacPro/Documents/NIMROD_DTI/SUBJECT/dmri/bvecs: No such
file or directory

The contents of that folder are: dwi_orig.mghdti.bvals dwi_orig.mghdti.bvecs 
dwi_orig.nii.gz dwi_orig_flip.nii.gz xfms

The full error message is enclosed with this email.

Thanks!

Best Wishes,
Elijah



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[Freesurfer] Mult-Shell Tracula Help

[Kristina Jelinkova]

Hello all,


I had a question regarding the program Tracula. I have two different DTI 
sequences that I wish to run (b=900 and b=2000) but am unsure at which step I 
am suppose to merge the two sequences together.


At this point, I have pre-processed each of the sequences separately using 
trac-all. Should I take each of the separate trac-all output data.nii.gz files, 
merge them, run bedpostX, and then run the ball-and-stick model fit on the new 
bedpostX output? Also, is there a way  to use nii.gz files in the configuration 
file rather than a dcm list?


Thank you in advance for your help!
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Re: [Freesurfer] ERROR: cannot unpack mosiacs without ASCII header

[Aloi, Joseph]

Excellent, thank you!  To do that, do I send an e-mail to the listserv with the 
log files attached or do I use the filedrop?


yea, can you post the log file of both the successful and failing runs?

On 05/19/2016 11:28 AM, Aloi, Joseph wrote:
>
> Hi Doug,
>
> No that’s not how I usually store my files- I have a folder for the
> particular study that I am working on then the dicoms for each subject
> in that study are stored in individual subject folders within the
> study folder.
>
> I got a chance to look around the recon-all logs this morning for a
> subject that I had successfully processed in the past (but that I get
> the error when I try to process this same dataset now).  From
> comparing the recon-all log from when recon-all ran successfully
> versus now, things are running fine up until it gets to MRI_convert.
> However, it looks like things are actually starting to go haywire
> during MRI_convert even before I get the warning about the ASCII
> header and recon-all exits.  It appears that MRI_convert is having
> some trouble with extracting some of the information it needs from the
> dicom file, resulting in the error that I posted.  I know you guys are
> busy, but would you be able to take a look at the log files?  I’ve
> only been using freesurfer a few weeks, so I would definitely
> appreciate any insights you might have from looking at the log files.
>
> Thank you!
>
> I don't have any idea what is going wrong. I noticed that the file
> that it is having problems with is here
> /Users/alojos/Applications/freesurfer/subjects/sub_.dcm
> Do you really keep all your dicom files in that location?
>
>
>
> On 05/17/2016 11:47 PM, Aloi, Joseph wrote:
> > Hi Doug,
> > Sorry- I've added entire correspondence onto the end of this
> e-mail.  I don't think the disk filled up as I am on a 3 TB hard drive
> and I still have ~2 TB of free space on my disk.  Anything else you
> think it could be?
> > Thanks!
> > Joseph Aloi
> > Please remember to include previous correspondence otherwise we can't
> > keep track of the problem!
> > Eg, I don't have the previous email to see what the error was. Is it
> > possible that the disk filled up?
> > On 05/17/2016 09:49 AM, Aloi, Joseph wrote:
> > > Hi Doug,
> > >
> > > Yes, you are correct- data I have previously processed without any
> > > problems is no longer being processed.
> > >
> > > My version of freesurfer is 5.3.0; I only downloaded it a few weeks
> > > ago so I have not changed my freesurfer version recently.
> > >
> > > Thanks!
> > >
> > > Joseph Aloi
> > > Graduate Student, MD/PhD Scholars Program
> > > Department of Pharmacology and Experimental Neuroscience
> > > University of Nebraska Medical Center
> > >
> > > Neurobehavioral Research Assistant, Center For Neurobehavioral
> Research
> > > Boys Town National Research Hospital
> > So the exact same data set is now generating an error whereas it ran
> > smoothly before? What version of FS are you using? Did you change
> versions?
> > doug
> > On 05/16/2016 09:49 AM, Aloi, Joseph wrote:
> > >
> > > Hi freesurfer experts,
> > >
> > > I have recently begun to use freesurfer to do structural MRI
> > > analyses.  I have been able to successfully process about 40
> > > structural scans with recon-all thus far, but starting a few days ago,
> > > I started getting this error whenever I run recon-all:
> > >
> > > WARNING: file
> > > /Users/alojos/Applications/freesurfer/subjects/sub_.dcm does not
> > > contain a Siemens ASCII header
> > >
> > > has this file been anonymized?
> > >
> > > ERROR: cannot unpack mosiacs without ASCII header
> > >
> > > Darwin nerc130622.local 14.5.0 Darwin Kernel Version 14.5.0: Mon Jan
> > > 11 18:48:35 PST 2016; root:xnu-2782.50.2~1/RELEASE_X86_64 x86_64
> > >
> > > recon-all -s sub_ exited with ERRORS at Mon May 16 08:43:24
> CDT 2016
> > >
> > > Here are a few of the troubleshooting steps I’ve tried to track down
> > > the cause of the error:
> > >
> > > -- Re-run recon-all with a couple of scans from my dataset that I have
> > > already successfully processed
> > >
> > > - - Re-run recon-all the same datasets but on a different computer
> > >
> > > - - Re-convert the scans from .ima files to dicoms in osirix, then
> > > run recon-all
> > >
> > >
> > > For all of these steps, I have gotten the exact same error message.
> > > The files should be anonymized, since I used osirix’s “anonymize and
> > > convert” function to generate the dicom files (the scans were given to
> > > me as .ima files).
> > >
> > > Any suggestions on what to try next?
> > >
> > > Thank you!
> > >
> > >
> > > Joseph Aloi
> > >
> > > The information in this e-mail may be privileged and confidential,
> > > intended only for the use of the addressee(s) above. Any unauthorized
> > > use or disclosure of this information is prohibited. If you have
> > > received this e-mail by mistake, please delete it and immediately
> > > contact the sender.
> > >
> > >
> > > 

[Freesurfer] R: R: Re: R: MASK.label from fsaverage to volume in subject space

[stdp82]

mri_label2label --srclabel rhrh.label --srcsubject fsaverage --trgsubject SUBJ 
--trglabel SUBJ_rhrh --regmethod surface --hemi rh

does not produce output.

Suggestions are very wellcome.

Thanks


Stefano


>Messaggio originale
>Da: std...@virgilio.it
>Data: 20-mag-2016 19.51
>A: 
>Ogg: [Freesurfer] R: Re: R: MASK.label from fsaverage to volume in subject 
space
>
>label2label and label2vol are options?
>
>mri_label2label --srclabel ROI.label --srcsubject fsaverage --trgsubject 
>Control61 --trglabel prova.label --hemi rh --regmethod surface
>
>I have tried the command line above ma the mask output is miss registered
>
>
>Stefano
>
>
>
>>Messaggio originale
>>Da: Bruce Fischl 
>>Data: 20-mag-2016 14.38
>>A: , "Freesurfer support list"edu>
>>Ogg: Re: [Freesurfer] R: MASK.label from fsaverage to volume in subject 
space
>>
>>sure, that should work
>>
>>cheers
>>Bruce
>>On Fri, 20 May 2016, std...@virgilio.it wrote:
>>
>>> Specifically, I have a .label from tksurfer and I would like to report 
this
>>> label on subj orig.nii.gz
>>>
>>>   Messaggio originale
>>>   Da: std...@virgilio.it
>>>   Data: 20-mag-2016 10.36
>>>   A: 
>>>   Ogg: [Freesurfer] MASK.label from fsaverage to volume in subject
>>>   space
>>> 
>>> Hi list,
>>> to trasform a MASK.label (created by tk surfer) from surface to volume
>>> is correct to use: 
>>> 
>>> 1. mri_surf2surf to register the mask from fsaverage to subj space
>>> 2. mri_surf2vol to report the label (subj space) to volume (subj
>>> space)
>>> 
>>> Thanks.
>>> 
>>> 
>>> Stefano
>>> 
>>> 
>>> 
>>>___
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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
>>dispose of the e-mail.
>>
>
>
>___
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[Freesurfer] R: Re: R: MASK.label from fsaverage to volume in subject space

[stdp82]

label2label and label2vol are options?

mri_label2label --srclabel ROI.label --srcsubject fsaverage --trgsubject 
Control61 --trglabel prova.label --hemi rh --regmethod surface

I have tried the command line above ma the mask output is miss registered


Stefano



>Messaggio originale
>Da: Bruce Fischl 
>Data: 20-mag-2016 14.38
>A: , "Freesurfer support list"
>Ogg: Re: [Freesurfer] R: MASK.label from fsaverage to volume in subject space
>
>sure, that should work
>
>cheers
>Bruce
>On Fri, 20 May 2016, std...@virgilio.it wrote:
>
>> Specifically, I have a .label from tksurfer and I would like to report this
>> label on subj orig.nii.gz
>>
>>   Messaggio originale
>>   Da: std...@virgilio.it
>>   Data: 20-mag-2016 10.36
>>   A: 
>>   Ogg: [Freesurfer] MASK.label from fsaverage to volume in subject
>>   space
>> 
>> Hi list,
>> to trasform a MASK.label (created by tk surfer) from surface to volume
>> is correct to use: 
>> 
>> 1. mri_surf2surf to register the mask from fsaverage to subj space
>> 2. mri_surf2vol to report the label (subj space) to volume (subj
>> space)
>> 
>> Thanks.
>> 
>> 
>> Stefano
>> 
>> 
>> 
>>___
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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
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Re: [Freesurfer] optimal T1 protocol

[Bruce Fischl]

Hi Jason

SMS/multi-band doesn't really help 3D sequences. I believe we have done 
ipat=3 and it has been fine, but perhaps Andre (or someone else who has 
gotten this type of data) can confirm?


cheers
Bruce


 On Fri, 20 May 2016, Jason Tourville wrote:


Hello freesurfer experts,
Do you have a recommended "optimal" T1 protocol on Bay 1 for cortical
reconstruction? 

For the past couple years, we've been using the 'tf1_mgh_multiecho_1mm_iso"
protocol which has PAT = 2 and a TA = 6:02. ??

I'm wondering if a faster option at the same resolution is now available
that is recon-approved? For instance, a multi-band option?  

Thanks for any feedback,
Jason



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Re: [Freesurfer] Cluster Color

[Timothy Hendrickson]

I'm just following up on this e-mail. I have not heard anything yet.

-Tim

On Mon, May 9, 2016 at 3:16 PM, Timothy Hendrickson 
wrote:

> Free Surfer Support,
>
> I have been using the command line version for group analysis since my
> data set has too many factors for QDEC.
>
> There are a few things that I enjoy about QDEC that I wish I could
> incorporate into the command line.
>
> 1) In QDEC the cluster color is not set arbitrarily, but rather based on
> significance.
>
> Is there any way to have the cluster color be set based on significance at
> command line?
>
> Is there a way to restrict the available colors that the clusters can be
> set as?
> Occasionally, cluster colors are a very similar color to the inflated
> underlay making it difficult to determine the outline of said cluster.
>
> 2) In QDEC one is able to visualize a scatter plot for a particular
> cluster. Is there any way to do this via the command line option?
>
> Thank you,
>
> -Tim Hendrickson
>
> --
> Timothy Hendrickson
> Department of Psychiatry
> University of Minnesota
> Mobile: 507-259-3434 (texts okay)
>



-- 
Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Mobile: 507-259-3434 (texts okay)
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[Freesurfer] optimal T1 protocol

[Jason Tourville]

Hello freesurfer experts,

Do you have a recommended "optimal" T1 protocol on Bay 1 for cortical
reconstruction?

For the past couple years, we've been using the 'tf1_mgh_multiecho_1mm_iso"
protocol which has PAT = 2 and a TA = 6:02. 

I'm wondering if a faster option at the same resolution is now available
that is recon-approved? For instance, a multi-band option?

Thanks for any feedback,
Jason
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Re: [Freesurfer] segfault using brainstem module from dev version

[Vincent Beliveau]

Hi Martin, 

Thank you for the feedback. Our version of FS 5.3 is the centos4 build
(which works perfectly) so I downloaded the same when got a copy of dev
(nightly build 05-11-16). However, I just tried the centos6 and the
brainstem module now works smoothly (including mri_robust_register).
There must be a difference between FS 5.3 centos4, dev centos4 and dev
centos6 but I have no clue of what that could be or if it even matters.
I thought you might like to know. 

Best, 

Vincent. 

On 17.05.2016 19:27, Martin Reuter wrote:

> Hi Vincent, 
> 
> I tried it on my machine and it works. No segfault and the registration looks 
> good. Is your dev version older? I don't specifically remember fixing 
> anything recently, but it may be best to download a more recent 
> robust_register binary? It could also be that something else is incompatible 
> on your system (e.g. different centos versions etc). 
> 
> Best, Martin
> 
> On 05/13/2016 10:29 AM, Vincent Beliveau wrote: 
> 
> Hi Martin, 
> 
> I assume you want the actual inputs, not the command, sorry about that ;) 
> I've attached the tmp folder created by the brainstem module. 
> 
> Best, 
> 
> Vincent. 
> 
> On 13.05.2016 16:21, Vincent Beliveau wrote: 
> 
> Hi Martin, 
> 
> Thanks for the help. From the brainstem-structures.log, mri_robust_register 
> is called by the brainstem module as follow: 
> 
> /data1/vbeliveau/software/freesurfer-Linux-centos4_x86_64-dev-110516/bin//mri_robust_register
>  --mov imageDump.mgz  --dst 
> /indirect/data1/vbeliveau/atlas/proc/MR/recon_final/f5249_GD/tmp/BS_T1based//BS-DE-binaryMask_autoCropped.mgz
>  -lta trash.lta --mapmovhdr imageDump_coregistered.mgz  --sat 50 
> 
> Best, 
> 
> Vincent 
> 
> On 13.05.2016 16:13, Martin Reuter wrote: Hi Eugenio and Vincent,
> 
> I cannot remember when I say robust_register crash the last time. It should 
> never happen. So it could also be that the inputs are already corrupted. Can 
> you send the inputs to that command so that I can try to replicate and see if 
> this is still a bug or what is going on?
> 
> Thanks, Martin
> 
> On 05/13/2016 09:54 AM, Eugenio Iglesias wrote: 
> 
> It seems that mri_robust_register crashed. Martin, any ideas? 
> The algorithm worked because the rough registration from the previous step 
> was apparently enough to yield a decent segmentation. 
> Maybe we should consider stopping the whole process if mri_robust_register 
> dies... 
> 
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com [1]
> www.bcbl.eu [2]
> 
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer [3] 
> 
> -
> 
> FROM: "Vincent Beliveau" 
> TO: "Freesurfer support list" 
> SENT: Friday, May 13, 2016 2:40:11 PM
> SUBJECT: [Freesurfer] segfault using brainstem module from dev version 
> 
> Hi list (and Eugenio), 
> 
> I've ran the brainstem module from the dev version on some data processed 
> with FS v5.3. The module created some great segmentations of brainstem but 
> when taking a closer look at the log file, there is 2 seg faults which occur 
> when calls to mri_robust_register are made, with the following output (full 
> log attached, see line 319 and 371): 
> 
> /data1/vbeliveau/software/freesurfer-Linux-centos4_x86_64-dev-110516/bin//mri_robust_register:
>  line 3: 36835 Segmentation fault mri_robust_register.bin "$@"
> /data1/vbeliveau/software/freesurfer-Linux-centos4_x86_64-dev-110516/bin//mri_robust_register
>  --mov imageDump.mgz --dst 
> /indirect/data1/vbeliveau/atlas/proc/MR/recon_final/f5249_GD/tmp/BS_T1based//BS-DE-binaryMask_autoCropped.mgz
>  -lta trash.lta --mapmovhdr imageDump_coregistered.mgz --sat 50: Segmentation 
> fault
> mv: cannot stat ?imageDump_coregistered.mgz?: No such file or directory 
> 
> I'm curious about how is this affecting the overall process, as otherwise 
> everything appears to be working smoothly. 
> 
> Best, 
> 
> Vincent. 
> 
> -- 
> Vincent Beliveau, MSc
> Neurobiology Research Unit 
> Juliane Maries Vej 28, 3rd floor
> Rigshospitalet, building 6931
> DK-2100 Copenhagen, Denmark 
> 
> phone:  +45 3545 6718
> e-mail: vincent.beliv...@nru.dk 
> ___
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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
> dispose of the e-mail. 
> 
> -- 
> Martin Reuter, PhD
> Assistant Professor of Radiology, Harvard Medical School
> Assistant Professor of Neurology, Harvard Medical School
> A.A.Martinos Center for 

[Freesurfer] Question about group analysis

[Josh Gray]

Hello,

I've got a very basic question related to group analysis. If I want run a
correlation of voxels in the cortex with a variable *controlling *for
another continous variable, how do I do this. I know how to run them both
in a GLM simultaneously by coding the matrix 0 1 1, however, how do I look
at the first variable after controlling for the other? Here is an example
of my current fsgd input (I want to control for income):


  GroupDescriptorFile 1
  Title MyTitle
  Class Class1 plus blue
  CLASS Class2 circle green
  SomeTag
  Variables impulsivity  income
  Input subjid1 Main   10100
  Input subjid2 Main   20200
  etc.
-- 
Graduate Student
Psychology Dept. - Clinical Program
Experimental & Clinical Psychopharmacology Laboratory
University of Georgia
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Re: [Freesurfer] R: MASK.label from fsaverage to volume in subject space

[Bruce Fischl]

sure, that should work

cheers
Bruce
On Fri, 20 May 2016, std...@virgilio.it wrote:


Specifically, I have a .label from tksurfer and I would like to report this
label on subj orig.nii.gz

  Messaggio originale
  Da: std...@virgilio.it
  Data: 20-mag-2016 10.36
  A: 
  Ogg: [Freesurfer] MASK.label from fsaverage to volume in subject
  space

Hi list,
to trasform a MASK.label (created by tk surfer) from surface to volume
is correct to use: 

1. mri_surf2surf to register the mask from fsaverage to subj space
2. mri_surf2vol to report the label (subj space) to volume (subj
space)

Thanks.


Stefano



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[Freesurfer] R: MASK.label from fsaverage to volume in subject space

[stdp82]

Specifically, I have a .label from tksurfer and I would like to report this 
label on subj orig.nii.gz




Messaggio originale

Da: std...@virgilio.it

Data: 20-mag-2016 10.36

A: 

Ogg: [Freesurfer] MASK.label from fsaverage to volume in subject space



Hi list,
to trasform a MASK.label (created by tk surfer) from surface to volume is 
correct to use: 
1. mri_surf2surf to register the mask from fsaverage to subj space2. 
mri_surf2vol to report the label (subj space) to volume (subj space)
Thanks.

Stefano



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[Freesurfer] MASK.label from fsaverage to volume in subject space

[stdp82]

Hi list,
to trasform a MASK.label (created by tk surfer) from surface to volume is 
correct to use: 
1. mri_surf2surf to register the mask from fsaverage to subj space2. 
mri_surf2vol to report the label (subj space) to volume (subj space)
Thanks.

Stefano___
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Re: [Freesurfer] create a table from measures under multiple subjects

[Liu Y]

Dear Douglas,
I used mri_segstats --annot to create the measures. If
aparcstats2table works, how to let the program know which subjects,
which path, and which file should use? Yawu


On Thu, May 19, 2016 at 6:08 PM, Douglas N Greve 
wrote:

> How did you create the measures? If with mris_anatomical_stats, then use
> can use aparcstats2table
>
> On 05/19/2016 03:06 AM, Liu Y wrote:
> > Hi Freesurfers,
> > I calculated the thicknesses of a cluster for some subjects, and each
> > of the measure was saved under each subject' s folder. How to create a
> > table containing all the measures? What is the command?
> > Thanks,
> > Yawu
> >
> >
> >
> > ___
> > 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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>
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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
dispose of the e-mail.