[Freesurfer] Error running recon-all

[vin rasa]

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Dear Freesurfer experts,
Greetings!


In the first minute of recon-all, we are getting following error:

mghRead(/media/results/mri/rawavg.mgz): could not read 262144 bytes at
slice 0


T1 data type is int16, data type 4 (looked using fslinfo)

Looking forward to have your input!

Thank you so much,
Kind regards
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Re: [Freesurfer] T1 orientation prior to running recon-all

[Bruce Fischl]

Hi Abid

nope, you shouldn't have to, as long as the header info is correct. Does it 
come up properly in freeview? That is, does what freeview thinks the 
orientations are match what they really are?


cheers
Bruce
On Wed, 
24 Jul 2019, Abid Qureshi wrote:




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Dear Freesurfer,
Does my T1 MPRAGE need to be in a particular orientation prior to running
recon-all? Meaning should I use mri_convert to change to RAS orientation to
avoid any L/R confusion with the output measures.

For instance, mri_info says the orientation: 
MPRAGE = LPS
orig.mgz = LIA
T1.mgz = LIA

I'm confused because if you bring up an image in freeview, say the T1.mgz,
it uses the RAS coordinate system.

Thanks,
Abid

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[Freesurfer] T1 orientation prior to running recon-all

[Abid Qureshi]

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Dear Freesurfer,

Does my T1 MPRAGE need to be in a particular orientation prior to running
recon-all? Meaning should I use mri_convert to change to RAS orientation to
avoid any L/R confusion with the output measures.

For instance, mri_info says the orientation:
MPRAGE = LPS
orig.mgz = LIA
T1.mgz = LIA

I'm confused because if you bring up an image in freeview, say the T1.mgz,
it uses the RAS coordinate system.

Thanks,
Abid
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Re: [Freesurfer] Multiple overlays onto surface

[Bruce Fischl]

Hi Zeynab

tksurfer has been deprecated for years. Can you use freeview instead? You 
can do this in freeview by loading one as a "curvature" map and the other 
as an overlay


cheers
Bruce


On Wed, 24 Jul 2019, Alshelh, Zeynab 
wrote:



Hi Freesurfers,

Is it possible to view two overlays on one surface image using TkSurfer? One
of the surface overlays is binary while the other isn't. I have been able to
load them both onto TkSurfer but I can only view one at a time. 

Kind regards,



Zeynab Alshelh, PhD | Postdoctoral Research Fellow

Pain and Neuroinflammation Imaging Laboratory


Harvard Medical School | A. A. Martinos Center for Biomedical Imaging
| Massachusetts General Hospital | 149 Thirteenth Street, Room 1101
| Charlestown, MA 02129

+1 (617) 794 6838

zalsh...@mgh.harvard.edu | www.nmr.mgh.harvard.edu


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Re: [Freesurfer] label to asc

[Bruce Fischl]

Hi Sam

they are not the same. A label is just a list of vertices in the surface 
(with some possibly voxel coordinates and also with a single value/vertex). 
It doesn't have to be ever vertex in the surface, and also contains no 
information about topology (e.g. which vertices are connected by an edge)


cheers
Bruce


On Wed, 24 Jul 2019, Sam W. wrote:



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Thanks Bruce. Can I ask you a very basic question? What exactly is the
difference between a surface and a label file? I thought the difference was
that the label file is just a normal text file containing the vertices that
are used to construct a surface. If so, is there a tool that allows me to
create a surface from a label file? mri_label2surf would be my first guess,
but that doesn't seem to exist.
Best regards,
Sam


On Wed, Jul 24, 2019 at 4:18 PM Bruce Fischl 
wrote:
  Hi Sam

  the labels are already ascii

  cheers
  Bruce
  On Tue, 23 Jul 2019, Sam W. wrote:

  >
  > External Email - Use Caution
  >
  > Hi,
  >
  > Is it possible to convert a label file like rh.cuneus.label
  into asc? I
  > tried
  > mris_convert --label rh.cuneus.label ctx-rh-cuneus rh.white
  rh.cuneus.asc
  >
  > but got an error:
  >  
  > ERROR: unknown file annot file type specified for output:
  rh.cuneus.asc
  >
  > Thanks!
  > Sam
  >
  >
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Re: [Freesurfer] Mass-Univariate LME - help please!

[tom parker]

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Dear Kersten,

Thank you so much for the quick reply! It was really helpful!!
I still have a couple of doubts regarding the visualization of the results
if you don't mind.

After running the last command *fs_write_Y(sided_pval,mri,'**spval_lh.mgh')*,
I tried to visualize the results with *tksurfer fsaverage lh inflated
-overlay spval_lh.mgh -fthresh 1.3* (1.3 was the pth value that came out
from lme_mass_FDR2) but there were no clusters on the surface.

If I run mri_surfcluster with spval_lh.mgh as input it seems there are 15
clusters, here is a sample of the first clusters that come out:
# ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZNVtxs
WghtVtx
   11.000   8  22284.41 -2.28.6   -3.3  48988
46268.86
   21.000  140211   1542.44 -8.2  -16.7   58.6   3024
2633.36
   31.000   44065   1510.18-16.3  -71.7   -4.6   2078
1810.43
  (...)

Am I doing something wrong?

I also tried the spatiotemporal mass-univariate approach that you suggested
but matlab gets stuck with this command:
[lhRgs,lhRgMeans] = lme_mass_RgGrow(lhsphere,lhRe,lhTh0,lhcortex,2,95);

In the terminal it says:
"Starting region growing algorithm
Computing seeds ..."

Do you have any suggestions on how to solve this?

Thanks again for the help!


Hi Tom,

basically most of it looks OK to me, just a few remarks:

I assume that you deliberately chose the plain mass-univariate approach
instead of the potentially more powerful spatiotemporal mass-univariate
approach.

For the interpretation of the intercepts, if desired, it may be
advantageous to code sex as 0 and 1, and de-mean age. But that's not
strictly necessary.

I suspect that it's just a typo, so just for the sake of completeness: for
contrast estimation, I don't think that using CM.C1, CM.C2, etc. would
work, as the program expects a 'C' substructure. So instead, one would use
CM1.C, CM2.C etc for the different contrasts, if I am not mistaken.

About the mri_surfcluster command: if you want to do the FDR2 inference as
suggested by the LME tutorial, just use the 'pth' value as returned by the
lme_mass_FDR2 script for thresholding. I believe that you are mixing
different kinds of inference (traditional FDR, clusterwise) otherwise.

Finally, if you want to make corrected inferences for the whole cortex,
it's probably better to compute one (FDR2) threshold for both hemispheres
at once (see the very last part of the tutorial) instead of treating them
separately.

And regarding your specific questions:

The order is fine.

You can visualize the 'spval_lh.mgh' by first loading e.g. the
'lh.inflated' surface of the fsaverage template, and then adding
'spval_lh.mgh' as an overlay. Same with e.g. 'rh.inflated' for the
'spval_rh.mgh' file.

About the Monte Carlo correction for this type of analysis others may know
better, sorry.

Best regards,

Kersten

Missatge de tom parker  del dia dg., 21 de jul.
2019 a les 20:50:

> Dear all,
>
> I am currently running a Mass-Univariate LME analysis in Freesurfer. I
> have some doubts about the last steps and I was wondering whether someone
> could help me figure them out and also check what I have done so far (sorry
> for the long email).
>
> My study has 2 time points (baseline, follow-up), 3 groups (controls,
> patients without cognitive problems, patients with cognitive problems) and
> 2 covariates of no interest (age, sex).
> I am interested in looking at the interactions between group and time
> (mainly whether the 2 patient groups show more cortical thinning over time
> compared to controls).
>
> These are the commands I have ran so far through terminal or in matlab:
>
> 1)
> mris_preproc --qdec-long long.qdec.table.dat --target fsaverage --hemi lh
> --meas thickness --out lh.thickness.mgh
> mris_preproc --qdec-long long.qdec.table.dat --target fsaverage --hemi rh
> --meas thickness --out rh.thickness.mgh
>
> 2)
> mri_surf2surf --hemi lh --s fsaverage --sval lh.thickness.mgh --tval
> lh.thickness_sm15.mgh --fwhm-trg 15 --cortex  --noreshape
> mri_surf2surf --hemi rh --s fsaverage --sval rh.thickness.mgh --tval
> rh.thickness_sm15.mgh --fwhm-trg 15 --cortex  --noreshape
>
> 3)
> [Y,mri] = fs_read_Y('lh.thickness_sm15.mgh');
> [Y,mri] = fs_read_Y('rh.thickness_sm15.mgh');
>
> 4)
> lhsphere = fs_read_surf('fsaverage/surf/lh.sphere')
> rhsphere = fs_read_surf('fsaverage/surf/rh.sphere')
> lhcortex = fs_read_label('fsaverage/label/lh.cortex.label')
> rhcortex = fs_read_label('fsaverage/label/rh.cortex.label')
>
> 5) Create X matrix in matlab, here is a sample:
> intercept time  group2 group2*time group3
> group3*time   age  sex
> 1 0   0  0  0
>   0 41   1
> 1 2.42  0  0  0
>   0 41   1
> 1 0   1  0  0
>   0

[Freesurfer] Multiple overlays onto surface

[Alshelh, Zeynab]

Hi Freesurfers,

Is it possible to view two overlays on one surface image using TkSurfer? One of 
the surface overlays is binary while the other isn't. I have been able to load 
them both onto TkSurfer but I can only view one at a time.

Kind regards,




Zeynab Alshelh, PhD | Postdoctoral Research Fellow

Pain and Neuroinflammation Imaging Laboratory


Harvard Medical School | A. A. Martinos Center for Biomedical Imaging | 
Massachusetts General Hospital | 149 Thirteenth Street, Room 1101 | 
Charlestown, MA 02129

+1 (617) 794 6838

zalsh...@mgh.harvard.edu | www.nmr.mgh.harvard.edu
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[Freesurfer] (no subject)

[fsbuild]

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Hello Sebastian,
Please download the zip archive from the following link,
https://drive.google.com/file/d/1w0vZyWTY0HrbcDiP1jWsmGl_GMUSh7tR/view?usp=sharing
Then expand and read the README.patch file and follow the instructions. 
When you are done, you should be able to launch freeview by double clicking on 
the icon of the application bundle in the Finder.

- R.

On Jul 24, 2019, at 05:51, Cassel, Sebastian /DZNE 
sebastian.cas...@dzne.de wrote:Dear all,based on this 
thread:https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-April/051591.htmlIs
 there any update for this?I have a MacBookPro with MacOs Mojave (10.14.3) and 
I'm facing the same issue with FreeSurfer 6.0.0 stable.Start FreeView via 
launch pad is failing during loading a volume, starting it via terminal works 
perfectly 
fine.BestSebastianExternal
 Email - Use 
Caution___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] label to asc

[Sam W.]

External Email - Use Caution

Thanks Bruce. Can I ask you a very basic question? What exactly is the
difference between a surface and a label file? I thought the difference was
that the label file is just a normal text file containing the vertices that
are used to construct a surface. If so, is there a tool that allows me to
create a surface from a label file? mri_label2surf would be my first guess,
but that doesn't seem to exist.
Best regards,
Sam


On Wed, Jul 24, 2019 at 4:18 PM Bruce Fischl 
wrote:

> Hi Sam
>
> the labels are already ascii
>
> cheers
> Bruce
> On Tue, 23 Jul 2019, Sam W. wrote:
>
> >
> > External Email - Use Caution
> >
> > Hi,
> >
> > Is it possible to convert a label file like rh.cuneus.label into asc? I
> > tried
> > mris_convert --label rh.cuneus.label ctx-rh-cuneus rh.white rh.cuneus.asc
> >
> > but got an error:
> >
> > ERROR: unknown file annot file type specified for output: rh.cuneus.asc
> >
> > Thanks!
> > Sam
> >
> >
> >___
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Re: [Freesurfer] label to asc

[Bruce Fischl]

Hi Sam

the labels are already ascii

cheers
Bruce
On Tue, 23 Jul 2019, Sam W. wrote:



External Email - Use Caution

Hi,

Is it possible to convert a label file like rh.cuneus.label into asc? I
tried
mris_convert --label rh.cuneus.label ctx-rh-cuneus rh.white rh.cuneus.asc

but got an error:
 
ERROR: unknown file annot file type specified for output: rh.cuneus.asc

Thanks!
Sam


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Re: [Freesurfer] Cluster sizes discrepancy for mri_surfcluster vs mri_segstats

[Mark Wagshul]

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Doug,

We are still seeing differences, but I notice that the results from segstats 
are all whole integers, while the results from surfcluster (Max cluster size) 
is not.  I assume this is because surfcluster is using partial volume.  How do 
we implement this in segstats?

Thanks,

Mark
___
Mark Wagshul, PhD
Albert Einstein College of Medicine
Bronx, NY

Sent from my iPhone

> On Jul 18, 2019, at 11:50 AM, Greve, Douglas N.,Ph.D. 
>  wrote:
> 
> When you run mri_surfcluster, save an output cluster number (--ocn) 
> output, then feed that into mri_segstats.
> 
>> On 7/18/19 11:44 AM, Mark Wagshul wrote:
>> 
>> External Email - Use Caution
>> 
>> Hi.  I have a question about cluster size determination within Freesurfer.
>> 
>> We are running linear mixed model on our Freesurfer generated volume 
>> data over the left and right cortex parcellations, and would like to 
>> look at cluster size at the p < 0.01 cluster-forming threshold level.
>> 
>> 1)After running the models, we have created a .mgh image of the 
>> F-stats results, separately for the negative and positive results, 
>> saving them with fs_write_Y.
>> 
>> 2)We then run these data through mri_surfcluster, which reports the 
>> maximum cluster size of 216 voxels.  This was run with the command:
>> 
>> a.mri_surfcluster --hemi lh --in F_lhstats.mgh --o F_lhstats 
>> _negCluster.mgh --subject fsaverage --thmin 6.8 --sign pos
>> 
>> b.The “sign” is set to positive because this is running on F-numbers.
>> 
>> 3)Next, we run mri_segstats on the output of the last command to get 
>> the location and sizes of the individual clusters, as follows:
>> 
>> a.mri_segstats --seg F_lhstats _negCluster.mgh --annot lh.aparc.annot 
>> lh parc --slabel fsaverage lh --seg --sum F_lhstats_negCluster.txt
>> 
>> The problem is that this is the output of that file 
>> (F_lhstats_negCluster.txt):
>> 
>> # Title Segmentation Statistics
>> 
>> #
>> 
>> # generating_program mri_segstats
>> 
>> # cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
>> 
>> # cmdline mri_segstats --seg F_lhstats_negCluster.mgh --annot 
>> lh.aparc.annot lh parc --slabel fsaverage lh --seg --sum 
>> F_lhstats_negCluster.txt
>> 
>> # sysname  Linux
>> 
>> # hostname loginnode2
>> 
>> # machine  x86_64
>> 
>> # user mwagshul
>> 
>> # anatomy_type volume
>> 
>> #
>> 
>> # SUBJECTS_DIR /home/mrrc-all/MRE_LAB/Holtzer/QdecAnalysis
>> 
>> # subjectname fsaverage
>> 
>> # SegVolFile F_lhstats_negCluster.mgh
>> 
>> # SegVolFileTimeStamp  2019/07/18 11:21:52
>> 
>> # Annot fsaverage lh parc
>> 
>> # Label fsaverage lh --seg
>> 
>> # ExcludeSegId
>> 
>> # Only reporting non-empty segmentations
>> 
>> # VoxelVolume_mm3 1
>> 
>> # TableCol  1 ColHeader Index
>> 
>> # TableCol  1 FieldName Index
>> 
>> # TableCol  1 Units NA
>> 
>> # TableCol  2 ColHeader SegId
>> 
>> # TableCol  2 FieldName Segmentation Id
>> 
>> # TableCol  2 Units NA
>> 
>> # TableCol  3 ColHeader NVoxels
>> 
>> # TableCol  3 FieldName Number of Voxels
>> 
>> # TableCol  3 Units unitless
>> 
>> # TableCol  4 ColHeader Volume_mm3
>> 
>> # TableCol  4 FieldName Volume
>> 
>> # TableCol  4 Units mm^3
>> 
>> # TableCol  5 ColHeader StructName
>> 
>> # TableCol  5 FieldName Structure Name
>> 
>> # TableCol  5 Units NA
>> 
>> # NRows 8
>> 
>> # NTableCols 5
>> 
>> # ColHeaders  Index SegId NVoxels Volume_mm3 StructName
>> 
>>   1   0161454   161454.0  Seg
>> 
>> *2   6   524  524.0  Seg0006*
>> 
>> *  3   7   897  897.0  Seg0007*
>> 
>> *  4   8   413  413.0  Seg0008*
>> 
>> *  5   9   311  311.0  Seg0009*
>> 
>> *  6  10   165  165.0  Seg0010*
>> 
>> *  7  1161   61.0  Seg0011*
>> 
>> *  8  1217   17.0  Seg0012*
>> 
>> This clearly is reporting clusters larger than the 216 voxels reported 
>> by mri_surfcluster.  Hope someone can help us figure out the 
>> discrepancy here, thanks!
>> 
>> (As an aside, what are we doing wrong with the mri_segstats command 
>> which is not printing out the actual anatomical locations for each 
>> cluster?).
>> 
>> Mark
>> 
>> 
>> Mark Wagshul, PhD
>> Associate Professor
>> Gruss Magnetic Resonance Research Center
>> Albert Einstein College of Medicine
>> Bronx, NY 10461
>> 
>> Ph: 718-430-4011
>> 
>> FAX: 718-430-3399
>> 
>> Email: mark.wags...@einstein.yu.edu 
>> 
>> einstein-logo-rgb
>> 
>> This email message and any accompanying attachments may contain 
>> privileged information intended only for the named recipient(s). If 
>> you are not the intended recipient(s), you are hereby notified that 
>> the dissemination, distribution, and or copying of this message is 
>> strictly prohibited. If you receive this message in error, or are not 
>> the named recipient(s), please notify the sender at the email address 
>> above, delete this email from your computer, and 

[Freesurfer] WG: Update FreeView on MacOs

[Cassel, Sebastian /DZNE]

Dear all,

 

based on this thread:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-April/051591.htm
l

 

Is there any update for this?

I have a MacBookPro with MacOs Mojave (10.14.3) and I'm facing the same
issue with FreeSurfer 6.0.0 stable.

 

Start FreeView via launch pad is failing during loading a volume, starting
it via terminal works perfectly fine.

 

Best

Sebastian

 



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