[Freesurfer] New to Freesurfer; cortical thickness

[Marja Caverlé]

Hi All,

I am new to Freesurfer and I would like to use it for a project I am
working on right now. For this project I have two patient groups of which I
have structural MRI scans and a lot of other measures. I hope to get
cortical thickness numbers from the scans and compare these with the other
measures.

Anyway, I am trying to get something done in Freesurfer and it does not
really seem to work. I assume I have to do a recon-all -all, but when I try
this, I get an error saying that the flag is unrecognised. It probably is a
small error, easy to solve, but I already get stuck on it since I am
totally new to Freesurfer.

Could anyone help me out?
Some of my questions are;

- Am I correct that recon-all -all already coregisters the scans to
template?
- What will be the outcome? Will I get pictures, or a table with numbers,
and if it is a table, which area's are specified? I have a list of ROIs,
but how do I let Freesurfer know I am interested in those areas?
- Can I do recon-all -all on a folder with all my patients, or do I have to
do it one by one? (There not that much, approximately 12 scans)
- Can I do recon-all -all on .nii.gz files? The originals are DICOM, but
the problem is that there is just one large DICOM folder, which does not
specify which files are part of which scan. I have converted them to
.nii.gz since I am a bit familiar with FSL, but I do not know whether this
actually works in Freesurfer.
- Why do I get the unrecognised flag error?

I apologise for these questions, they are probably very easy to answer, but
I just don't have a clue yet.

Thank you guys.

Best,

Marja
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[Freesurfer] request for corrected p-values for mni305 space

[Joseph Dien]

Hi,
   just a user request for corrected p-values for the mni305 space analyses 
(i.e., sig.voxel.nii.gz files).

Thanks!

Joe



Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
E-mail: jdie...@mac.com
Cell Phone: 202-297-8117
http://joedien.com

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Re: [Freesurfer] surfaces from 0.5mm scan

[Trisanna Sprung-Much]

thanks Dr. Fischl,

Would there be a reason as to why recon-all crashed when doing the
conformation then? I got the following error in my terminal:


Original Data has (0.5, 0.5, 0.5) mm size and (394, 466, 378) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from short to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to
/data-01/trisanna/freesurfer/MNI_average_2009b_asymm/mri/orig.mgz...

 mri_add_xform_to_header -c
/data-01/trisanna/freesurfer/MNI_average_2009b_asymm/mri/transforms/talairach.xfm
/data-01/trisanna/freesurfer/MNI_average_2009b_asymm/mri/orig.mgz
/data-01/trisanna/freesurfer/MNI_average_2009b_asymm/mri/orig.mgz

INFO: extension is mgz
#
#@# Talairach Tue May 24 19:10:10 EDT 2016
/data-01/trisanna/freesurfer/MNI_average_2009b_asymm/mri

 mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i
orig.mgz --o orig_nu.mgz


recon-all -s MNI_average_2009b_asymm exited with ERRORS at Tue May 24
19:11:34 EDT 2016



--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Wed, May 25, 2016 at 6:49 PM, Bruce Fischl 
wrote:

> Hi Trisanna
>
> you can use the -cm flag, but typically what we do is let recon-all
> "conform" the data to 1mm, then do a post-hoc surface deformation with
> the original highres data using mris_make_surfaces
>
> cheers
> Bruce
> On Wed, 25 May 2016, Trisanna Sprung-Much wrote:
>
> > Hi there
> >
> > My initial email didn't seem to have sent and so I am re-sending it:
> >
> > I would like to know if it is possible to create surfaces from a scan
> that
> > is 0.5mm isotropic. I tried to run recon-all on our MNI 2009b atlas
> which is
> > 0.5mm cubed and it crashed quite quickly afterwards. I wonder if this
> has to
> > do with the fact that Freesurfer tried to conform it to 1mm isotropic?
> >
> > When I ran recon-all on the 1mm atlas it created some nice surfaces.
> >
> > Let me know if you would like the .log as I cannot seem to make much
> sense
> > of it.
> >
> > best wishes
> >
> > Trisanna
> > --
> > Ph.D. CandidateMcGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> >
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Re: [Freesurfer] surfaces from 0.5mm scan

[Bruce Fischl]

Hi Trisanna

you can use the -cm flag, but typically what we do is let recon-all 
"conform" the data to 1mm, then do a post-hoc surface deformation with 
the original highres data using mris_make_surfaces

cheers
Bruce
On Wed, 25 May 2016, Trisanna Sprung-Much wrote:

> Hi there
> 
> My initial email didn't seem to have sent and so I am re-sending it:
> 
> I would like to know if it is possible to create surfaces from a scan that
> is 0.5mm isotropic. I tried to run recon-all on our MNI 2009b atlas which is
> 0.5mm cubed and it crashed quite quickly afterwards. I wonder if this has to
> do with the fact that Freesurfer tried to conform it to 1mm isotropic?
> 
> When I ran recon-all on the 1mm atlas it created some nice surfaces.
> 
> Let me know if you would like the .log as I cannot seem to make much sense
> of it.
> 
> best wishes
> 
> Trisanna
> --
> Ph.D. CandidateMcGill University
> Integrated Program in Neuroscience
> Psychology
> 
> 
>
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[Freesurfer] surfaces from 0.5mm scan

[Trisanna Sprung-Much]

Hi there

My initial email didn't seem to have sent and so I am re-sending it:

I would like to know if it is possible to create surfaces from a scan that
is 0.5mm isotropic. I tried to run recon-all on our MNI 2009b atlas which
is 0.5mm cubed and it crashed quite quickly afterwards. I wonder if this
has to do with the fact that Freesurfer tried to conform it to 1mm
isotropic?

When I ran recon-all on the 1mm atlas it created some nice surfaces.

Let me know if you would like the .log as I cannot seem to make much sense
of it.

best wishes

Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
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Re: [Freesurfer] Need Help

[HARI GURAGAIN]

Thanks a lot. It helped.
> On May 25, 2016, at 3:24 PM, Douglas N Greve  
> wrote:
> 
> recon-all -s yoursubjectname -i /path/to/one/dicomfile.dcm
> tksurfer yoursubjectname lh pial -ov 
> $SUBJECTS_DIR/yoursubjectname/surf/lh.thickness -fminmax .1 3
> 
> 
> On 05/24/2016 08:34 PM, HARI GURAGAIN wrote:
>> Hello,
>> 
>> I am kind of new to the neuroimaging. I was trying to reproduce the 
>> following type of figure in freesurfer (3d image with thickness). But 
>> I couldn’t do that. Is it possible for anyone  to explain how to 
>> generate such figure from mri data. Just to clarify, I have the mri 
>> data in the form of *.dcm. Is there any specific command to get 
>> through it? I tried to work on similar figures using tksurfer *** but 
>> couldn’t produce.
>> 
>> Your help is greatly appreciated.
>> Thank you,
>> 
>> Hari
>> unknown.tiff
>> This figure is from one paper.
>> Fig. 4. 3D models of the pial surfaces generated by FreeSurfer with a 
>> colored overlay of the local cortical thickness in mm. The top row 
>> shows the pial surfaces of the left and right
>> hemisphere based on data with an isotropic resolution of 0.5 mm and 
>> the bottom row with an isotropic resolution of 1 mm; both data sets 
>> have been acquired at 7 T.
>> 
>> 
>> 
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> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
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> 
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Re: [Freesurfer] Need Help

[Douglas N Greve]

recon-all -s yoursubjectname -i /path/to/one/dicomfile.dcm
tksurfer yoursubjectname lh pial -ov 
$SUBJECTS_DIR/yoursubjectname/surf/lh.thickness -fminmax .1 3


On 05/24/2016 08:34 PM, HARI GURAGAIN wrote:
> Hello,
>
> I am kind of new to the neuroimaging. I was trying to reproduce the 
> following type of figure in freesurfer (3d image with thickness). But 
> I couldn’t do that. Is it possible for anyone  to explain how to 
> generate such figure from mri data. Just to clarify, I have the mri 
> data in the form of *.dcm. Is there any specific command to get 
> through it? I tried to work on similar figures using tksurfer *** but 
> couldn’t produce.
>
> Your help is greatly appreciated.
> Thank you,
>
> Hari
> unknown.tiff
> This figure is from one paper.
> Fig. 4. 3D models of the pial surfaces generated by FreeSurfer with a 
> colored overlay of the local cortical thickness in mm. The top row 
> shows the pial surfaces of the left and right
> hemisphere based on data with an isotropic resolution of 0.5 mm and 
> the bottom row with an isotropic resolution of 1 mm; both data sets 
> have been acquired at 7 T.
>
>
>
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Re: [Freesurfer] White matter segmentation

[Douglas N Greve]

That link says to use mri_aparc2aseg, not mri_vol2vol

On 05/25/2016 11:21 AM, Mahmoudi, Fariborz wrote:
> I added --2009s to my command (mri_vol2vol) but it didn't give me the white 
> matter labels yet. I used following code can you tell me how should I modify 
> it?
>
> /usr/local/freesurfer/bin/recon-all -subjid $ID -autorecon1
> /usr/local/freesurfer/bin/recon-all -subjid $ID -autorecon2
> /usr/local/freesurfer/bin/recon-all -subjid $ID -autorecon3
>
> mri_vol2vol --mov ./FreeSurfer_Subjects/MGZ/${ID}/mri/aparc.a2009s+aseg.mgz  
> --targ ./FreeSurfer_Subjects/MGZ/${ID}/mri/rawavg.mgz --regheader --o 
> ./FreeSurfer_Subjects/MGZ/${ID}/mri/aparc.a2009s+aseg_org.mgz --a2009s 
> --no-save-reg --keep-precision --interp nearest
>
> Thanks,
> Fari
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Tuesday, May 24, 2016 6:45 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] White matter segmentation
>
> see
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_freesurfer-2540nmr.mgh.harvard.edu_msg47157.html=CwIBAg=aLnS6P8Ng0zSNhCF04OWImQ_He2L69sNWG3PbxeyieE=OSYmVYk3jPR6JSZwGSUjf1P4YyJXtRWvghayjS8UAMU=77QFGWjiRTdsKBaqbcq6AW2Nqzqwn4EZbuERJUedD-4=qMzdr2C1nZGoavb2EVn5mK_dvUu0JTNZ7dt3BHg6oGM=
>
>
> On 05/24/2016 05:44 PM, Mahmoudi, Fariborz wrote:
>> Dear All,
>>
>> I want to segment white matter into 131xx and 141xx label series. I
>> used aparc.a2009s but it just gave me cortex labels (111xx and 121xx).
>> Can  anyone guide me how could I do this?
>>
>> Regards,
>>
>> Fari
>>
>>
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
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> Fax: 617-726-7422
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Re: [Freesurfer] Tract length

[Alan Francis]

Hi Anthony -

Thanks for your input. You have raised very important points. I looked at
the literature and found a paper where they look at FBL - fiber bundle
length.

Lauren E. Salminen
,[image:
corresponding author] Peter R. Schofield
, Elizabeth
M. Lane , Jodi
M. Heaps ,
Kerrie
D. Pierce ,
Ryan
Cabeen , David
H. Laidlaw ,
Erbil Akbudak
, Thomas E.
Conturo ,
Stephen
Correia ,
and Robert H. Paul


Neuronal fiber bundle lengths in healthy adult carriers of the ApoE4
allele: A quantitative tractography DTI study

They call this method quantitative DTI where they looked at Fiber length,
volume etc. What they found is intriguing. I quote, "Results suggest that
FBL in the UF is influenced by the presence of an ApoE e4 allele (ApoE4) in
healthy older adults.


In my study, could it be that shorter FBL in the UF may predispose one to
Cannabis addiction? Just thinking out loud.

Thanks,

Alan


On Wed, May 25, 2016 at 10:52 AM, Anthony Dick  wrote:

> Hello,
>
> I wouldn't mind jumping on this issue more broadly. Diffusion indices like
> FA, ADC, RD, and AD have more clear physiologic correlates. But what does
> the length of a tract, the volume of a tract, or the number of streamlines
> say about physiology? Tract length seems to be very dependent on head size.
> Or, for example, a person with a long corticospinal tract might simply be
> taller. At the very least these indices should be included with nuisance
> variables controlling for brain size. Length and volume measures seem to be
> very much affected by pulse sequence parameters, further calling into
> question their utility (see Wang et al., 2012; doi:
> 10.1016/j.neuroimage.2011.12.062). However, tract volume at least makes
> more intuitive sense (for example, quantifying Wallerian degeneration in T1
> scans is essentially a volume measure). I thought Alan raised an important
> issue.
>
> Anthony
>
> On 5/25/16 10:34 AM, Alan Francis wrote:
>
>
> Hi Imagers -
>
> I am looking at the Uncinate fasciculus in a Cannabis use disorder (CUD).
> I found that CUD subjects have significantly shorter tract length  and a
> significant group x side interaction in comparison with controls. Have you
> seen this before? What is the interpretation of this finding?
>
> Thank you,
>
> Alan
>
>
>
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> --
> Anthony Steven Dick, Ph.D.
> Assistant Professor
> Director, Cognitive Neuroscience Program and Graduate Certificate in 
> Cognitive Neuroscience
> Department of Psychology
> Florida International University Modesto A. Maidique Campus AHC4 454
> 11200 S.W. 8th Street
> Miami, FL 33199
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> Email: ad...@fiu.edu
> Webpage: http://myweb.fiu.edu/adick
> Join the Society for the Study of Human Development: http://www.sshdonline.org
>
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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
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*Alan N. Francis PhD*
Instructor - Imaging Neuroscience
Brain Imaging Center
McLean Hospital
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115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu 

Re: [Freesurfer] errors in wm and pial boundaries

[Corinna Bauer]

Hi Bruce, just checking in to see if you have had an opportunity to take a
look at the data I sent over?

Thanks

Corinna

On Wed, May 18, 2016 at 6:19 PM, Corinna Bauer  wrote:

> Sure. I'm uploading now. The above is approximately slice 75, although the
> control points/wm surface problem is seen throughout in this subject.
>
> Thanks
>
> Corinna
>
> On Tue, May 17, 2016 at 3:46 PM, Bruce Fischl 
> wrote:
>
>> Hi Corinna
>>
>> it's hard to tell what's going on from a single slice. If you upload the
>> subject and tell us the specific coordinates that you see problems in we
>> will take a look
>>
>> cheers
>> Bruce
>> On Tue, 17 May 2016, Corinna Bauer wrote:
>>
>> Hello all,We are analyzing data from our collaborators and are running
>>> into
>>> some difficulties with the accuracy of the pial and wm boundaries. The
>>> wm.mgz appears to follow the actual WM, independent of the wm surface
>>> boundary. Attached is an example showing two types of problems.
>>> 1. the WM surface is inaccurate regardless of the number of control
>>> points
>>> used.
>>> 2. The pial surface is inaccurate, missing a bunch of the sulcal and
>>> gyral
>>> patterns of the left parietal lobe (see area around cursor).
>>>
>>> For completeness, I have also included the wm.mgz at the same slice.
>>>
>>> I should mention that these problems has been occurring in multiple
>>> subjects.
>>>
>>> Any suggestions??
>>>
>>> Thanks
>>>
>>> Corinna
>>>
>>>
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Re: [Freesurfer] FreeSurfer 5.3 OASIS

[Gouveia , Vítor]

Dear Bruce,

Thank you for your reply. I think I've just discovered the issue.
I was using Ubuntu 16.04 and it seems that FS does not work with Ubuntu
16.04.
I've just tried with Ubuntu 14.04 and FS is working. I'm now processing one
image.

The commands that I use:

recon-all -subjid fsresult -i OAS1_0001_MR1_mpr-1_anon.img
recon-all -all -subjid fsresult

Do you know if FS works with Ubuntu 16.04?

Cheers,
Vitor


On 25 May 2016 at 17:38, Bruce Fischl  wrote:

> HI Vitor
>
> can you send us your command line and full screen output? We definitely
> support img/hdr, but note that it may not contain enough info to figure out
> the true anatomical directions (e.g. left from right)
>
> cheers
> Bruce
>
> On Wed, 25 May 2016, Gouveia, Vítor wrote:
>
> Hello,
>> I've been trying to process a subject from the OASIS database with
>> FreeSurfer 5.3. FS is relative new to me. I'm trying to use recon-all with
>> -all but the format img/hdr does not seem supported. Do you have any ideia
>> what should I do to process these images?
>>
>> Thank you.
>>
>> Sincerely,
>> Vitor
>>
>>
>>
>>
>>
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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] DTI error

[Anastasia Yendiki]

Hi Jasmin - On my screen the dash "-" symbol before the "c" looks 
different than the one before "path". I'd check if you are indeed typing a 
plain "-c".


Best,
a.y

On Wed, 25 May 2016, Jasmin Alves wrote:


Hi Anastasia,
 I am still receiving the following error message when I run a different 
participant doing, trac-all -path –c
dmrirc1_sim.txt: 

ERROR: flag –c unrecognized

-path –c dmrirc1_sim.txt


If you have any ideas for what i can try it would be very appreciated!  


Thanks!

Jasmin 


On Sun, May 22, 2016 at 9:07 PM, Jasmin Alves  wrote:
  Correct. 

  On Sunday, May 22, 2016, Anastasia Yendiki  
wrote:

No idea, sorry. You used the -c option with the previous steps of 
trac-all and didn't see this
error, correct?

On Sun, 22 May 2016, Jasmin Alves wrote:

  Hi Anastasia,
  Perhaps I was asking for advice regarding the wrong step in 
trac-all, do you
  have any ideas why I am still receiving the following error:

  ERROR: flag –c unrecognized -path –c dmrirc1_sim.txt

  This occurs when I do trac-all -path –c dmrirc1_sim.txt

  I tried looking at posts from previous mailing lists, and 
found no match to
  this problem.


  Thank you,

  Jasmin


  On Sun, May 22, 2016 at 5:53 PM, Anastasia Yendiki
   wrote:

        Ok, then you can ignore the error that you see when you 
run the
        bedpost step.

        `On Sun, 22 May 2016, Jasmin Alves wrote:

        Sorry for the mix-up. All of the bedpost output files 
are
        generated as well
        both 1 and 2 of each file. 

        On Sun, May 22, 2016 at 4:22 PM, Anastasia Yendiki
         wrote:

              These are output files from the -prep step. I'm
        asking about
              output files from the bedpost step, since that's
        where you're
              encountering the error.

  
https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard

  
.edu_fswiki_trac-2Dall-23Outputsfromtrac-2Dall-2Dbedp=DQIDaQ=clK7kQUTWt

  
AVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=7c1gaW5UpDUs-D

  
f4uqLGaiN1YKi8WpD7PUUFUH_Yh_8=PDchguGtZxsQtn6Ikrgq51EI2N8a2zv32ihUs8-gVaA

              =
              What's in the dmri.bedpostX/ directory?

              On Sun, 22 May 2016, Jasmin Alves wrote:

                    Output files are being generated, ie.
                     1. dtifit_FA.nii.gz - Fractional Anisotropy
                     2. dtifit_MD.nii.gz - Mean Diffusivity
                     3. dtifit_MO.nii.gz - Mode of the 
Anisotropy
                     4. dtifit_S0.nii.gz - Non-Diffusion 
weighted
        image
                     5. dtifit_L1.nii.gz - Primary Eigenvalue
                     6. dtifit_L2.nii.gz - Secondary Eigenvalue
                     7. dtifit_L3.nii.gz - Tertiary Eigenvalue
                     8. dtifit_V1.nii.gz - Primary Eigenvector
                     9. dtifit_V2.nii.gz - Secondary Eigenvector
                    10. dtifit_V3.nii.gz - Tertiary Eigenvector
                    But it seems the bedpost process gets cut
        short and
                    then,  the trac-all path
                    step won't work. I have ran it a few times 
and
        the
                    bedpost step ends at the
                    same point. 


                    On Sun, May 22, 2016 at 3:24 PM, Anastasia
        Yendiki
                     wrote:

                          But do you see the output files from 
the
                    previous step? The
                          outputs from each step are described 
on
        the
                    wiki.

                          On Sun, 22 May 2016, Jasmin Alves 
wrote:

                                Hi Anastasia,
                                Thank you for the reply, when I 
do
        just
                    let it run,
        

Re: [Freesurfer] DTI error

[Jasmin Alves]

Good call! Thanks Anastasia! It worked!

On Wed, May 25, 2016 at 8:46 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Jasmin - On my screen the dash "-" symbol before the "c" looks
> different than the one before "path". I'd check if you are indeed typing a
> plain "-c".
>
> Best,
> a.y
>
>
> On Wed, 25 May 2016, Jasmin Alves wrote:
>
> Hi Anastasia,
>>  I am still receiving the following error message when I run a different
>> participant doing, trac-all -path –c
>> dmrirc1_sim.txt:
>>
>> ERROR: flag –c unrecognized
>>
>> -path –c dmrirc1_sim.txt
>>
>>
>> If you have any ideas for what i can try it would be very appreciated!
>>
>>
>> Thanks!
>>
>> Jasmin
>>
>>
>> On Sun, May 22, 2016 at 9:07 PM, Jasmin Alves  wrote:
>>   Correct.
>>
>>   On Sunday, May 22, 2016, Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu> wrote:
>>
>> No idea, sorry. You used the -c option with the previous
>> steps of trac-all and didn't see this
>> error, correct?
>>
>> On Sun, 22 May 2016, Jasmin Alves wrote:
>>
>>   Hi Anastasia,
>>   Perhaps I was asking for advice regarding the wrong
>> step in trac-all, do you
>>   have any ideas why I am still receiving the following
>> error:
>>
>>   ERROR: flag –c unrecognized -path –c dmrirc1_sim.txt
>>
>>   This occurs when I do trac-all -path –c dmrirc1_sim.txt
>>
>>   I tried looking at posts from previous mailing lists,
>> and found no match to
>>   this problem.
>>
>>
>>   Thank you,
>>
>>   Jasmin
>>
>>
>>   On Sun, May 22, 2016 at 5:53 PM, Anastasia Yendiki
>>    wrote:
>>
>> Ok, then you can ignore the error that you see
>> when you run the
>> bedpost step.
>>
>> `On Sun, 22 May 2016, Jasmin Alves wrote:
>>
>> Sorry for the mix-up. All of the bedpost output
>> files are
>> generated as well
>> both 1 and 2 of each file.
>>
>> On Sun, May 22, 2016 at 4:22 PM, Anastasia Yendiki
>>  wrote:
>>
>>   These are output files from the -prep step.
>> I'm
>> asking about
>>   output files from the bedpost step, since
>> that's
>> where you're
>>   encountering the error.
>>
>>
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard
>>
>>
>> .edu_fswiki_trac-2Dall-23Outputsfromtrac-2Dall-2Dbedp=DQIDaQ=clK7kQUTWt
>>
>>
>> AVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=7c1gaW5UpDUs-D
>>
>>
>> f4uqLGaiN1YKi8WpD7PUUFUH_Yh_8=PDchguGtZxsQtn6Ikrgq51EI2N8a2zv32ihUs8-gVaA
>>
>>   =
>>   What's in the dmri.bedpostX/ directory?
>>
>>   On Sun, 22 May 2016, Jasmin Alves wrote:
>>
>> Output files are being generated, ie.
>>  1. dtifit_FA.nii.gz - Fractional
>> Anisotropy
>>  2. dtifit_MD.nii.gz - Mean
>> Diffusivity
>>  3. dtifit_MO.nii.gz - Mode of the
>> Anisotropy
>>  4. dtifit_S0.nii.gz - Non-Diffusion
>> weighted
>> image
>>  5. dtifit_L1.nii.gz - Primary
>> Eigenvalue
>>  6. dtifit_L2.nii.gz - Secondary
>> Eigenvalue
>>  7. dtifit_L3.nii.gz - Tertiary
>> Eigenvalue
>>  8. dtifit_V1.nii.gz - Primary
>> Eigenvector
>>  9. dtifit_V2.nii.gz - Secondary
>> Eigenvector
>> 10. dtifit_V3.nii.gz - Tertiary
>> Eigenvector
>> But it seems the bedpost process gets
>> cut
>> short and
>> then,  the trac-all path
>> step won't work. I have ran it a few
>> times and
>> the
>> bedpost step ends at the
>> same point.
>>
>>
>> On Sun, May 22, 2016 at 3:24 PM,
>> Anastasia
>> Yendiki
>>  wrote:
>>
>>   But do you see the output files
>> from the
>> previous step? The
>>   outputs from each step are

Re: [Freesurfer] DTI error

[Jasmin Alves]

Hi Anastasia,

 I am still receiving the following error message when I run a different
participant doing, trac-all -path –c dmrirc1_sim.txt:

ERROR: flag –c unrecognized

-path –c dmrirc1_sim.txt


If you have any ideas for what i can try it would be very appreciated!


Thanks!

Jasmin

On Sun, May 22, 2016 at 9:07 PM, Jasmin Alves  wrote:

> Correct.
>
>
> On Sunday, May 22, 2016, Anastasia Yendiki 
> wrote:
>
>>
>> No idea, sorry. You used the -c option with the previous steps of
>> trac-all and didn't see this error, correct?
>>
>> On Sun, 22 May 2016, Jasmin Alves wrote:
>>
>> Hi Anastasia,
>>> Perhaps I was asking for advice regarding the wrong step in trac-all, do
>>> you
>>> have any ideas why I am still receiving the following error:
>>>
>>> ERROR: flag –c unrecognized -path –c dmrirc1_sim.txt
>>>
>>> This occurs when I do trac-all -path –c dmrirc1_sim.txt
>>>
>>> I tried looking at posts from previous mailing lists, and found no match
>>> to
>>> this problem.
>>>
>>>
>>> Thank you,
>>>
>>> Jasmin
>>>
>>>
>>> On Sun, May 22, 2016 at 5:53 PM, Anastasia Yendiki
>>>  wrote:
>>>
>>>   Ok, then you can ignore the error that you see when you run the
>>>   bedpost step.
>>>
>>>   `On Sun, 22 May 2016, Jasmin Alves wrote:
>>>
>>>   Sorry for the mix-up. All of the bedpost output files are
>>>   generated as well
>>>   both 1 and 2 of each file.
>>>
>>>   On Sun, May 22, 2016 at 4:22 PM, Anastasia Yendiki
>>>    wrote:
>>>
>>> These are output files from the -prep step. I'm
>>>   asking about
>>> output files from the bedpost step, since that's
>>>   where you're
>>> encountering the error.
>>>
>>>
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard
>>>
>>>
>>> .edu_fswiki_trac-2Dall-23Outputsfromtrac-2Dall-2Dbedp=DQIDaQ=clK7kQUTWt
>>>
>>>
>>> AVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=7c1gaW5UpDUs-D
>>>
>>>
>>> f4uqLGaiN1YKi8WpD7PUUFUH_Yh_8=PDchguGtZxsQtn6Ikrgq51EI2N8a2zv32ihUs8-gVaA
>>>
>>> =
>>> What's in the dmri.bedpostX/ directory?
>>>
>>> On Sun, 22 May 2016, Jasmin Alves wrote:
>>>
>>>   Output files are being generated, ie.
>>>1. dtifit_FA.nii.gz - Fractional Anisotropy
>>>2. dtifit_MD.nii.gz - Mean Diffusivity
>>>3. dtifit_MO.nii.gz - Mode of the Anisotropy
>>>4. dtifit_S0.nii.gz - Non-Diffusion weighted
>>>   image
>>>5. dtifit_L1.nii.gz - Primary Eigenvalue
>>>6. dtifit_L2.nii.gz - Secondary Eigenvalue
>>>7. dtifit_L3.nii.gz - Tertiary Eigenvalue
>>>8. dtifit_V1.nii.gz - Primary Eigenvector
>>>9. dtifit_V2.nii.gz - Secondary Eigenvector
>>>   10. dtifit_V3.nii.gz - Tertiary Eigenvector
>>>   But it seems the bedpost process gets cut
>>>   short and
>>>   then,  the trac-all path
>>>   step won't work. I have ran it a few times and
>>>   the
>>>   bedpost step ends at the
>>>   same point.
>>>
>>>
>>>   On Sun, May 22, 2016 at 3:24 PM, Anastasia
>>>   Yendiki
>>>    wrote:
>>>
>>> But do you see the output files from the
>>>   previous step? The
>>> outputs from each step are described on
>>>   the
>>>   wiki.
>>>
>>> On Sun, 22 May 2016, Jasmin Alves wrote:
>>>
>>>   Hi Anastasia,
>>>   Thank you for the reply, when I do
>>>   just
>>>   let it run,
>>>   I get the following
>>>   error when I try to do trac-all
>>>   -path –c
>>>   dmrirc1_sim.txt
>>>
>>>   I get the following error:
>>>
>>>   ERROR: flag –c unrecognized
>>>
>>>   -path –c dmrirc1_sim.txt
>>>
>>>
>>>   Thanks,
>>>
>>>   Jasmin
>>>
>>>
>>>   On Sun, May 22, 2016 at 1:51 AM,
>>>   Anastasia Yendiki
>>>   
>>>   wrote:
>>>
>>> Hi Jasmin - Check if things
>>>   are
>>>   running
>>>   despite that error. Are
>>> output files being
>>>   generated?
>>>
>>> a.y
>>>
>>> On Sat, 21 May 2016, Jasmin
>>>   Alves

Re: [Freesurfer] FreeSurfer 5.3 OASIS

[Bruce Fischl]

HI Vitor

can you send us your command line and full screen output? We definitely 
support img/hdr, but note that it may not contain enough info to figure 
out the true anatomical directions (e.g. left from right)


cheers
Bruce
On Wed, 25 May 
2016, Gouveia, Vítor wrote:



Hello,
I've been trying to process a subject from the OASIS database with
FreeSurfer 5.3. FS is relative new to me. I'm trying to use recon-all with
-all but the format img/hdr does not seem supported. Do you have any ideia
what should I do to process these images?

Thank you.

Sincerely,
Vitor


  

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