[Freesurfer] Centre on label double click in freeview

[Chris Adamson]

Thanks for putting in the "centre over label" feature in Freeview.

Dr Chris Adamson
Senior Research Officer
Developmental Imaging, Clinical Sciences

Murdoch Childrens Research Institute
The Royal Children's Hospital
Flemington Road, Parkville, VIC 3052 Australia
E chris.adam...@mcri.edu.au
www.mcri.edu.au


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[Freesurfer] Fwd: recon-all -localGI with longitudinal pipeline output

[Mihaela Stefan]

Hello FreeSurfers,

I am trying to run recon-all -s  -localGI on a longitudinal dataset
but I get this error:

ERROR: Are you trying to run or re-run a longitudinal time point?
   If so, please specify the following parameters:

   \' -long   \'

   where  is the time point id (SAME as cross sectional
   ID) and  is the ID created in the -base run.
   The directory .long. will be created
   automatically or used for output, if it already exists.

Do I really need these if I want to run -localGI or for some reason
recon-all thinks that I am trying to re-run the longitudinal pipeline? I
renamed the folder replacing "long" (e.g. *OAS2_0001_MR1.new.OAS2_0001
instead of **OAS2_0001_MR1.long.OAS2_0001* ) and recon-all -localGI seems
to work.

Is there a better way to do this?

Thanks!
Mihaela
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Re: [Freesurfer] Edits to Aseg in the Longitudinal Stream

[Antonin Skoch]

Dear Tamara,

I presume that you edited your reconstruction in "Long" (=3rd) stage of 
longitudinal stream (recon-all -long )?.

If this is the case, I think that you can use

recon-all -long tpN1 templateID -autorecon2-wm -autorecon3

or

recon-all -long tpN1 templateID -autorecon2-noaseg -autorecon3

(effectively both commands are equivalent, they run the same steps).

where tpN1 is name of your directory defining cross-sectional recon (1st stage) 
and templateID is name of directory of your base (created in stage 2).

See
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits#RerunningEditsCommands

Regards,

Antonin Skoch


Hello,

After I make edits to my aseg output in the longitudinal stream, do I just
run the following command to recreate the final volumes:recon-long 
-autorecon2-noaseg -subjid 

I assume the -subjid is the name of the edited time point and  is
the name of the recreated volumes?

Thank you,
Tamara
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Re: [Freesurfer] Longitudinal stream with v6 but cross with v5.3

[Matthieu Vanhoutte]

Dear Antonin,

Thanks for the advices.

Best,
Matthieu

> Le 30 janv. 2017 à 17:45, Antonin Skoch  a écrit :
> 
> Dear Matthieu,
> 
> your issue is discussed here:
> 
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51092.html
> 
> and indirectly also here:
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg5.html
> 
> I think that with V6.0 you maybe could get slightly better results (some bugs 
> have been fixed and some tools improved), but definitelly it would require to 
> re-inspect your data after reprocessing.
> 
> Antonin Skoch
> 
> 
> Dear experts,
> 
> Does anybody could answer my last request ?
> Best,
> Matthieu
> 
> 2017-01-26 9:58 GMT+01:00 Matthieu Vanhoutte :
> 
> > Dear FS's experts,
> >
> > I have run all my cross with v5.3 and hesitate to run all longitudinal
> > process with v6. Does that make sense and will improve the process or would
> > it be risky to do this ?
> >
> > Many thanks for your lights !
> >
> > Best regards,
> > Matthieu
> 
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[Freesurfer] Edits to Aseg in the Longitudinal Stream

[Tamara Tavares]

Hello,

After I make edits to my aseg output in the longitudinal stream, do I just
run the following command to recreate the final volumes:

recon-long -autorecon2-noaseg -subjid 

I assume the -subjid is the name of the edited time point and  is
the name of the recreated volumes?

Thank you,
Tamara
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Re: [Freesurfer] Fw: Issue with creating inflated surface - poor surface registration?

[Saltzman, David]

We adjusted the offset and that was clearly the problem. Looks like it worked 
great. Thank you so much for clearing this up!


David Saltzman


Lab Manager

Language and Brain Laboratory

Department of Speech, Language, & Hearing Sciences

University of Connecticut



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: Monday, January 30, 2017 12:01:15 PM
To: Freesurfer support list
Cc: Rothermich, Kathrin
Subject: Re: [Freesurfer] Fw: Issue with creating inflated surface - poor 
surface registration?

Hi David

I'm not sure that there is anything actually wrong, I think what you are
seeing is just a visualization issue. The inflated surfaces
will overlap when viewed together in freeview, since they are
centered on each hemi and inflated. You can use the :offset=x,y,z modifier
for the -f ?h.inflated to move them left/right so they don't overlap if you
want.

cheers
Bruce


On Mon, 30 Jan 2017, Saltzman, David wrote:

>
> Hello FreeSurfer Developers,
>
>
> We have attempted to run the standard recon-all pipeline on multiple MRI
> datasets, and seem to be encountering the same error. While the recon-all
> log does not indicate there are any errors (so far as we can tell as
> novices), when we look at the inflated surfaces, there is clearly some
> problem creating the inflated surface, in that the hemispheres appeared to
> be mirrored. For the purpose of simplicity, we will include the log and scan
> information for the most recent anatomical scan we have to run the recon-all
> pipeline on. I believe the attached screenshot (anterior coronal view) will
> make the issue more apparent.
>
> 1) FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0 2) Platform:
> Mac OS 10.12
> 3) recon-all.log: see attached
> 4) Command run: recon-all -i "inputfile.nii" -subject subj1 -cortparc2
> -parcstats2 -aparc2aseg -all -3T (scans were performed on a 3T scanner)
> 5) Scan information:
> Data Axes Tilt:  Oblique (15.784 deg. from plumb)
> Data Axes Approximate Orientation:
>   first  (x) = Anterior-to-Posterior
>   second (y) = Superior-to-Inferior
>   third  (z) = Right-to-Left   [-orient ASR]
> R-to-L extent:   -80.718 [R] -to-94.282 [L] -step- 1.000 mm [176
> voxels]
> A-to-P extent:  -188.767 [A] -to-58.233 [P] -step- 1.000 mm [248
> voxels]
> I-to-S extent:  -186.650 [I] -to-68.350 [S] -step- 1.000 mm [256
> voxels]
>
> Any help would be tremendously appreciated!
>
> Thanks,
>
>
> David Saltzman
>
>
> Lab Manager
>
> Language and Brain Laboratory
>
> Department of Speech, Language, & Hearing Sciences
>
> University of Connecticut
>
>
>
>
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Re: [Freesurfer] problem with qdec

[Douglas N Greve]

On 01/29/2017 10:33 AM, Eva Wiedemann wrote:
> Dear freesurfer-users,
>
> I want to run a qdec analysis, comparing cortical thickness between 
> two groups and using age and gender as nuisance factors. those factors 
> are included in my data.table but when i want to chose the design i 
> can only select gender as a discrete factor and not as a nuisance 
> factor (see images attached).
No images attached, but it is probably not an issue. When you include 
gender as a factor, the results will be controlled for gender, it does 
not matter whether it is listed as a nuisance variable or not.
> The second problem I have is, when displaying the results, I can't 
> change the threshold. I can mark them but not change them. All the 
> other buttons in the window work though.
This is a hard bug to track down as it is obviously working on other 
platforms. Zeke, have you seen this problem before?
> Thanks for your help in advance!
> Yours sincerely, Eva Wiedemann
>
> PS: I'm using freesurfer v.5.3.0 on Ubuntu 15.10.
>
>
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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
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Re: [Freesurfer] QDEC - Controlling for gender

[Douglas N Greve]

I just tried normalizing the BDI and age on the fsgd file that you sent, 
and it did work. Can you double check? If it is still not working, then 
send both the fsgd file and the Xg.dat file


On 01/27/2017 05:06 PM, Jennifer Szeto wrote:
>
>
> *From:*Jennifer Szeto 
> *Sent:* 24 January 2017 23:31
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] QDEC - Controlling for gender
>
> Hi Doug,
>
>
> That doesn't seem to work either? Is there anything else I should 
> try/ does my fsgd file look alright?
>
>
> Thanks for your help,
>
> Jen
>
>
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> *Sent:* 24 January 2017 04:28
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] QDEC - Controlling for gender
> Have you tried normalizing BDI and age? By normalizing, I mean
> subtracting the mean and dividing by the stddev
>
>
> On 01/20/2017 05:46 PM, Jennifer Szeto wrote:
> >
> > Sorry, hope this is the right one!
> >
> >
> > Thanks,
> >
> > Jen
> >
> >
> >
> > 
> > *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> >  on behalf of Douglas Greve
> > 
> > *Sent:* 20 January 2017 22:26
> > *To:* freesurfer@nmr.mgh.harvard.edu
> > *Subject:* Re: [Freesurfer] QDEC - Controlling for gender
> >
> > sorry, I wanted the y.fsgd file from the qdec output directory
> >
> >
> > On 1/20/17 4:46 PM, Jennifer Szeto wrote:
> >>
> >> Thank you very much Doug,
> >>
> >>
> >> Please find attached the files I have been using to run the QDEC
> >> analyses.
> >>
> >>
> >> Jen
> >>
> >>
> >>
> >> 
> 
> >> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> >>  on behalf of Douglas Greve
> >> 
> >> *Sent:* 20 January 2017 15:27
> >> *To:* freesurfer@nmr.mgh.harvard.edu
> >> *Subject:* Re: [Freesurfer] QDEC - Controlling for gender
> >>
> >> can you send the fsgd file?
> >>
> >>
> >> On 1/20/17 6:54 AM, Jennifer Szeto wrote:
> >>>
> >>> Thanks Doug,
> >>>
> >>>
> >>> That seem to work for some of my variables (e.g. depression) when I
> >>> put gender and diagnosis as fixed factors, depression as covariate,
> >>> and age as nuisance factor but not for others (e.g. anxiety). I keep
> >>> getting error messages when trying to run some of my variables as
> >>> covariates (please see attached). Is there anything I can do to fix
> >>> this?
> >>>
> >>>
> >>> Thanks,
> >>> Jen
> >>>
> >>> 
> 
> >>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> >>>  on behalf of Douglas N
> >>> Greve 
> >>> *Sent:* 19 January 2017 21:48
> >>> *To:* freesurfer@nmr.mgh.harvard.edu
> >>> *Subject:* Re: [Freesurfer] QDEC - Controlling for gender
> >>> Just include it as a categorical factor. When you look at your 
> contrast
> >>> of interest, it will be with respect to regressing out gender
> >>>
> >>>
> >>> On 01/15/2017 08:55 PM, Jennifer Szeto wrote:
> >>> >
> >>> > Hi Freesurfer experts,
> >>> >
> >>> >
> >>> > I am trying to compare cortical thickness between groups while
> >>> > controlling for age and gender using QDEC. However, _gender_ is not
> >>> > showing up as a covariate variable or a nuisance factor (only 
> showing
> >>> > up as a fixed factor), I am wondering how I could control for gender
> >>> > in this case?
> >>> >
> >>> >
> >>> > Thank you very much,
> >>> >
> >>> > Jen
> >>> >
> >>> >
> >>> >
> >>> > ___
> >>> > Freesurfer mailing list
> >>> > Freesurfer@nmr.mgh.harvard.edu
> >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> Freesurfer Info Page - mail.nmr.mgh.harvard.edu 
> 
> mail.nmr.mgh.harvard.edu
> To see the collection of prior postings to the list, visit the 
> Freesurfer Archives. A searchable archive which of messages PRIOR to 
> March 2004 is at ...
>
>
>
> >>> Freesurfer Info Page - Harvard University
> >>> 
> Freesurfer Info Page - mail.nmr.mgh.harvard.edu 
> 
> mail.nmr.mgh.harvard.edu
> To see the collection of prior postings to the list, visit the 
> Freesurfer Archives. A searchable archive which of messages PRIOR to 
> March 2004 is at ...
>
>
>
> >>> mail.nmr.mgh.harvard.edu
> >>> To see the collection of prior postings to the list, visit the
> >>> Freesurfer Archives. A searchable archive which of messages PRIOR to
> >>> March 2004 is 

Re: [Freesurfer] Edits to White Matter

[Douglas N Greve]

Which volume are you re-creating? Changing the wm.mgz will not affect 
the aparc+aseg much (except through changes to the surface. The white 
surface may or may not change much, depending.


On 01/27/2017 03:33 PM, Gundel, Tristan J wrote:
> Hello,
>
> The link below will allow you to see the subject in question. It 
> contains the anonymized verson of the original T1 image, as well as 
> all of the corresponding masks and surfaces created with freesurfer. 
> The particular area we are having issues with is located around (8.01, 
> -45.57, 41.95). Any insight you could provide us about how to ensure 
> that the aparc+aseg.mgz and wm.mgz correspond accordingly would be 
> much appreciated. Thank you!
>
> https://ucsf.box.com/s/cmsk4di0q4b5u7e3oxutp1d19ds314h4
>
> Best Regards,
> Tristan
> 
> *From:* Gundel, Tristan J
> *Sent:* Tuesday, November 15, 2016 9:22 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Edits to White Matter
>
> Hello,
>
>I work in a lab that is currently using the Freesurfer algorithm to 
> collect data from MRI images of individuals with Multiple Sclerosis. 
> In order to increase the precision of our white matter masks we have 
> combined your algorithm with ANTS, hoping to achieve more accurate 
> surface volumes and aparc+aseg masks.
>Unfortunately we have had some issues when we edit our ANTS white 
> matter mask (using value of 255) and then put it through freesurfer 
> again, re-running recon-all (recon-all -autorecon2 -wm -autorecon3 -w 
> ). Our wm_surface and aparc+aseg mask do not change based on 
> the edits we have made, and do not follow the white matter volume 
> surface volume. How can we be sure that our white matter mask, and the 
> edits we make to it, are considered in the creation of wm_surface and 
> aparc+aseg mask? Please let me know if any of this is unclear and I 
> will explain it in more detail.
>
> Thank you,
> Tristan
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Fw: Issue with creating inflated surface - poor surface registration?

[Douglas N Greve]

let me know if the problem is the visualization as Bruce suggests. If 
not, I'll take a look


On 01/30/2017 12:00 PM, Saltzman, David wrote:
>
> Hopefully I did this correctly: 
> http://gate.nmr.mgh.harvard.edu/filedrop2/?p=49h8h1nu06w
>
>
> Thanks!
>
>
> David Saltzman
>
>
> /Lab Manager/
>
> Language and Brain Laboratory
>
> Department of Speech, Language, & Hearing Sciences
>
> University of Connecticut
>
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> *Sent:* Monday, January 30, 2017 11:55:47 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Fw: Issue with creating inflated surface - 
> poor surface registration?
> Can you upload that subject to our filedrop? See below for link
>
>
> On 01/30/2017 11:19 AM, Saltzman, David wrote:
> >
> > Hello FreeSurfer Developers,
> >
> >
> > We have attempted to run the standard recon-all pipeline on multiple
> > MRI datasets, and seem to be encountering the same error. While the
> > recon-all log does not indicate there are any errors (so far as we can
> > tell as novices), when we look at the inflated surfaces, there is
> > clearly some problem creating the inflated surface, in that the
> > hemispheres appeared to be mirrored. For the purpose of simplicity, we
> > will include the log and scan information for the most recent
> > anatomical scan we have to run the recon-all pipeline on. I believe
> > the attached screenshot (anterior coronal view) will make the issue
> > more apparent.
> >
> > 1) FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0
> > 2) Platform: Mac OS 10.12
> > 3) recon-all.log: see attached
> > 4) Command run: recon-all -i "inputfile.nii" -subject subj1 -cortparc2
> > -parcstats2 -aparc2aseg -all -3T (scans were performed on a 3T scanner)
> > 5) Scan information:
> > Data Axes Tilt:  Oblique (15.784 deg. from plumb)
> > Data Axes Approximate Orientation:
> >   first  (x) = Anterior-to-Posterior
> >   second (y) = Superior-to-Inferior
> >   third  (z) = Right-to-Left   [-orient ASR]
> > R-to-L extent:   -80.718 [R] -to-94.282 [L] -step- 1.000 mm
> > [176 voxels]
> > A-to-P extent:  -188.767 [A] -to-58.233 [P] -step- 1.000 mm
> > [248 voxels]
> > I-to-S extent:  -186.650 [I] -to-68.350 [S] -step- 1.000 mm
> > [256 voxels]
> >
> > Any help would be tremendously appreciated!
> >
> > Thanks,
> >
> >
> > David Saltzman
> >
> >
> > /Lab Manager/
> >
> > Language and Brain Laboratory
> >
> > Department of Speech, Language, & Hearing Sciences
> >
> > University of Connecticut
> >
> >
> >
> >
> > ___
> > 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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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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Re: [Freesurfer] Fw: Issue with creating inflated surface - poor surface registration?

[Bruce Fischl]

Hi David

I'm not sure that there is anything actually wrong, I think what you are 
seeing is just a visualization issue. The inflated surfaces 
will overlap when viewed together in freeview, since they are 
centered on each hemi and inflated. You can use the :offset=x,y,z modifier 
for the -f ?h.inflated to move them left/right so they don't overlap if you 
want.


cheers
Bruce


On Mon, 30 Jan 2017, Saltzman, David wrote:



Hello FreeSurfer Developers,


We have attempted to run the standard recon-all pipeline on multiple MRI
datasets, and seem to be encountering the same error. While the recon-all
log does not indicate there are any errors (so far as we can tell as
novices), when we look at the inflated surfaces, there is clearly some
problem creating the inflated surface, in that the hemispheres appeared to
be mirrored. For the purpose of simplicity, we will include the log and scan
information for the most recent anatomical scan we have to run the recon-all
pipeline on. I believe the attached screenshot (anterior coronal view) will
make the issue more apparent.

1) FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0 2) Platform:
Mac OS 10.12
3) recon-all.log: see attached
4) Command run: recon-all -i "inputfile.nii" -subject subj1 -cortparc2
-parcstats2 -aparc2aseg -all -3T (scans were performed on a 3T scanner)
5) Scan information: 
Data Axes Tilt:  Oblique (15.784 deg. from plumb)
Data Axes Approximate Orientation:
  first  (x) = Anterior-to-Posterior
  second (y) = Superior-to-Inferior
  third  (z) = Right-to-Left   [-orient ASR]
R-to-L extent:   -80.718 [R] -to-    94.282 [L] -step-     1.000 mm [176
voxels]
A-to-P extent:  -188.767 [A] -to-    58.233 [P] -step-     1.000 mm [248
voxels]
I-to-S extent:  -186.650 [I] -to-    68.350 [S] -step-     1.000 mm [256
voxels]

Any help would be tremendously appreciated!

Thanks,


David Saltzman


Lab Manager

Language and Brain Laboratory

Department of Speech, Language, & Hearing Sciences

University of Connecticut



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Re: [Freesurfer] Fw: Issue with creating inflated surface - poor surface registration?

[Saltzman, David]

Hopefully I did this correctly: 
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=49h8h1nu06w


Thanks!


David Saltzman


Lab Manager

Language and Brain Laboratory

Department of Speech, Language, & Hearing Sciences

University of Connecticut



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N Greve 

Sent: Monday, January 30, 2017 11:55:47 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fw: Issue with creating inflated surface - poor 
surface registration?

Can you upload that subject to our filedrop? See below for link


On 01/30/2017 11:19 AM, Saltzman, David wrote:
>
> Hello FreeSurfer Developers,
>
>
> We have attempted to run the standard recon-all pipeline on multiple
> MRI datasets, and seem to be encountering the same error. While the
> recon-all log does not indicate there are any errors (so far as we can
> tell as novices), when we look at the inflated surfaces, there is
> clearly some problem creating the inflated surface, in that the
> hemispheres appeared to be mirrored. For the purpose of simplicity, we
> will include the log and scan information for the most recent
> anatomical scan we have to run the recon-all pipeline on. I believe
> the attached screenshot (anterior coronal view) will make the issue
> more apparent.
>
> 1) FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0
> 2) Platform: Mac OS 10.12
> 3) recon-all.log: see attached
> 4) Command run: recon-all -i "inputfile.nii" -subject subj1 -cortparc2
> -parcstats2 -aparc2aseg -all -3T (scans were performed on a 3T scanner)
> 5) Scan information:
> Data Axes Tilt:  Oblique (15.784 deg. from plumb)
> Data Axes Approximate Orientation:
>   first  (x) = Anterior-to-Posterior
>   second (y) = Superior-to-Inferior
>   third  (z) = Right-to-Left   [-orient ASR]
> R-to-L extent:   -80.718 [R] -to-94.282 [L] -step- 1.000 mm
> [176 voxels]
> A-to-P extent:  -188.767 [A] -to-58.233 [P] -step- 1.000 mm
> [248 voxels]
> I-to-S extent:  -186.650 [I] -to-68.350 [S] -step- 1.000 mm
> [256 voxels]
>
> Any help would be tremendously appreciated!
>
> Thanks,
>
>
> David Saltzman
>
>
> /Lab Manager/
>
> Language and Brain Laboratory
>
> Department of Speech, Language, & Hearing Sciences
>
> University of Connecticut
>
>
>
>
> ___
> 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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Re: [Freesurfer] Fw: Issue with creating inflated surface - poor surface registration?

[Douglas N Greve]

Can you upload that subject to our filedrop? See below for link


On 01/30/2017 11:19 AM, Saltzman, David wrote:
>
> Hello FreeSurfer Developers,
>
>
> We have attempted to run the standard recon-all pipeline on multiple 
> MRI datasets, and seem to be encountering the same error. While the 
> recon-all log does not indicate there are any errors (so far as we can 
> tell as novices), when we look at the inflated surfaces, there is 
> clearly some problem creating the inflated surface, in that the 
> hemispheres appeared to be mirrored. For the purpose of simplicity, we 
> will include the log and scan information for the most recent 
> anatomical scan we have to run the recon-all pipeline on. I believe 
> the attached screenshot (anterior coronal view) will make the issue 
> more apparent.
>
> 1) FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0
> 2) Platform: Mac OS 10.12
> 3) recon-all.log: see attached
> 4) Command run: recon-all -i "inputfile.nii" -subject subj1 -cortparc2 
> -parcstats2 -aparc2aseg -all -3T (scans were performed on a 3T scanner)
> 5) Scan information:
> Data Axes Tilt:  Oblique (15.784 deg. from plumb)
> Data Axes Approximate Orientation:
>   first  (x) = Anterior-to-Posterior
>   second (y) = Superior-to-Inferior
>   third  (z) = Right-to-Left   [-orient ASR]
> R-to-L extent:   -80.718 [R] -to-94.282 [L] -step- 1.000 mm 
> [176 voxels]
> A-to-P extent:  -188.767 [A] -to-58.233 [P] -step- 1.000 mm 
> [248 voxels]
> I-to-S extent:  -186.650 [I] -to-68.350 [S] -step- 1.000 mm 
> [256 voxels]
>
> Any help would be tremendously appreciated!
>
> Thanks,
>
>
> David Saltzman
>
>
> /Lab Manager/
>
> Language and Brain Laboratory
>
> Department of Speech, Language, & Hearing Sciences
>
> University of Connecticut
>
>
>
>
> ___
> 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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Re: [Freesurfer] Longitudinal stream with v6 but cross with v5.3

[Antonin Skoch]

Dear Matthieu,

your issue is discussed here:

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51092.html

and indirectly also here:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg5.html

I think that with V6.0 you maybe could get slightly better results (some bugs 
have been fixed and some tools improved), but definitelly it would require to 
re-inspect your data after reprocessing.

Antonin Skoch


Dear experts,

Does anybody could answer my last request ?Best,
Matthieu

2017-01-26 9:58 GMT+01:00 Matthieu Vanhoutte :

> Dear FS's experts,
>
> I have run all my cross with v5.3 and hesitate to run all longitudinal
> process with v6. Does that make sense and will improve the process or would
> it be risky to do this ?
>
> Many thanks for your lights !
>
> Best regards,
> Matthieu
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Re: [Freesurfer] Time Series Revision in FS-Fast

[Douglas Greve]

sorry, you can't exclude time points from just part of the brain


On 1/30/17 5:28 AM, pfannmo...@uni-greifswald.de wrote:
> Dear Experts,
>
> I have a question concerning the evaluation of the time series in the FS-Fast 
> stream. There is one time series for each vertex of a brain. Can single time 
> points or series of time points be excluded from the analysis in the 
> following way: Remove time point 10 from the time series of vertex 220 and 
> time point 550 from vertex 42.
>
> This means a time point exclude file can not be used in my case. Can I 
> achieve this removal by setting the value of the time points to not-a-number 
> or something similar?
>
> Yours pfannmoe
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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>
>

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Re: [Freesurfer] Longitudinal stream with v6 but cross with v5.3

[Matthieu Vanhoutte]

Dear experts,

Does anybody could answer my last request ?

Best,
Matthieu

2017-01-26 9:58 GMT+01:00 Matthieu Vanhoutte :

> Dear FS's experts,
>
> I have run all my cross with v5.3 and hesitate to run all longitudinal
> process with v6. Does that make sense and will improve the process or would
> it be risky to do this ?
>
> Many thanks for your lights !
>
> Best regards,
> Matthieu
>
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Re: [Freesurfer] longitudinal tracula error

[Bárbara Avelar Pereira]

Hi Anastasia,

Thanks again for the help! And congrats on tracula — it's a great tool, and the 
online support is really good :)

I do have a follow-up question, if that’s OK. I’m currently running bedpost, 
and it gives the following error:

(…)
53 slices processed
54 slices processed
54 slices processed
55 slices processed
Queuing post processing stage
64 slices processed
For some reason the bedpostX process DOES NOT appear to have successfully 
completed. Please examine your results carefully.
/usr/local/freesurfer/bin/bedpostx_mgh: line 345: kill: (21128) - No such 
process

I was not running this on a cluster, but I was running a few subjects at the 
same time so I was wondering if it could be a memory problem? Or a 
compatibility problem between FSL and freesurfer?

It seems strange that it shows the same slice more than once on the monitor. 
But from what I read, the monitor is not entirely reliable and the best way to 
check whether everything ran smoothly is to look at the output. I have all the 
files that should have been created, but I’m still suspicious that something 
might be wrong. For example, my merged_xxx files are 50 volumes (should they 
have the same number of volumes as my original nii file? Because this is not 
the case...).

I’ve also tried running it directly from the command line and the error is the 
same (however, since this is longitudinal, when running bedpost from the 
command line, can I simply run it for each timepoint separately as if it was 
cross-sectional or is there an extra step?)

Many thanks!

On 26 Jan 2017, at 14:51, Yendiki, Anastasia 
> wrote:

Glad to hear it, thanks for checking! If the final 6.0 works, there's no need 
to dig up the beta.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
[freesurfer-boun...@nmr.mgh.harvard.edu]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se]
Sent: Thursday, January 26, 2017 3:29 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your help! Sorry for the delay in replying -- just wanted to 
make sure the was problem was indeed solved. Since I'm using a server for which 
I have no administrative rights, I had to wait before the update was installed. 
It seems to run perfectly now.
I can't find the beta version I was using at the time (just deleted it once I 
realised I was having the same problem), but if I manage to trace it back, I'll 
let you know.

Once again, thanks, I'm super grateful!


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
[freesurfer-boun...@nmr.mgh.harvard.edu]
 on behalf of Yendiki, Anastasia 
[ayend...@mgh.harvard.edu]
Sent: Sunday, January 22, 2017 7:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Barbara - If you're using the 5.3 version, then you'll have to download the 
update from 2014:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

This should fix the problem. But if there's a version of the 6.0 beta that was 
having the same problem, please let me know (by sending the trac-all copy of 
that version) so I can fix that asap.

Thanks!

a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
[freesurfer-boun...@nmr.mgh.harvard.edu]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se]
Sent: Friday, January 20, 2017 7:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your quick reply. I've only tried version 6.0 to determine 
whether the error was possibly version-related, but that doesn’t seem to be the 
case… I'm actually working with version 5.3 so I'll send attach the 
trac-all.local-copy for that if that’s OK. Once again, thank you!

On 20 Jan 2017, at 23:52, Yendiki, Anastasia 
> wrote:

Hi Barbara - If you take out the "set baselist" part, you'll run the 
cross-sectional TRACULA stream, i.e., analyze each time point independently. So 
you want to leave that in to use the longitudinal TRACULA stream.

The base template itself (i.e., the median of the T1s of the time-points) may 
not be used, but the files under the base template's directory are used. 
Longitudinal TRACULA maps between the base space to the space of each DWI time 
point, as described in the paper.

Can you please attach the file scripts/trac-all.local-copy? Since there's no 
official 6.0 version yet but multiple beta 

[Freesurfer] mri_cvs_register: how to read/import .m3z warp file

[Stefano Zappalà]

Dear FreeSurfer Developers,

I am trying to visualize and modify the output warp field (in .m3z) of a 
mri_cv_registration call aimed at aligning a T1w scan to the MNI space.

I was wondering how file format .m3z is organized, in order to read it with, 
for example, matlab. Or if there are simpler file format to convert the warp 
field to.

No information about it seems to be reported in the website. Moreover, I've 
searched the list and a similar question was not answered. I was wondering  if 
you have some suggestions in reading the output warp field of mri_cvs_register.

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
2) Platform: ubuntu 16.04 LTS

Many thanks,
Stefano.

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[Freesurfer] Time Series Revision in FS-Fast

[pfannmoelj]

Dear Experts,

I have a question concerning the evaluation of the time series in the FS-Fast 
stream. There is one time series for each vertex of a brain. Can single time 
points or series of time points be excluded from the analysis in the following 
way: Remove time point 10 from the time series of vertex 220 and time point 550 
from vertex 42.

This means a time point exclude file can not be used in my case. Can I achieve 
this removal by setting the value of the time points to not-a-number or 
something similar?   

Yours pfannmoe
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Re: [Freesurfer] FLAIR in hippocampus subfield segmentation

[Iglesias Gonzalez, Eugenio]

The answer is yes to both questions.
We thought for a while of naming the option 
-hippocampal-subfields-T1-additionalModality instead of 
-hippocampal-subfields-T1T2, but it looked too long and ugly.
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 28 Jan 2017, at 08:09, tulu 
> wrote:

Dear Freesurfer experts
Under Freesurfer V6 version, could the hippocampus subfield segmentation use 
high resolution FLAIR image ? if yes, is the command line  
-hippocampal-subfields-T1T2 ?
Thanks
JLH
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