[Freesurfer] re-calculating stats based on an updated ?h.pial surface

[Dominic Brendon Dwyer]

Hi all, 

 

We're using a tool which allows direct alteration of the pial surface
(http://sites.google.com/site/vxxsoftware/) resulting in another ?h.pial
file being created. We've found that it is a good way to both decrease
and increase the pial boundary where there are errors. The current
procedure is to use mris_fill once the surfaces are created and then
apply this to the brainmask.mgz before re-running recon2.

 

I was wondering if it was possible to recalculate the surface stats
based on an altered ?h.pial file without running recon2 again? The
reason being is that if the surface is extended rather than reduced then
it will not necessarily appear in the updated pial surface. 

 

Any help would be greatly appreciated. 

 

Many thanks,

 

Dominic

Melbourne Neuropsychiatry Centre

 

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Re: [Freesurfer] Cannot allocate memory

[Douglas Greve]

 How was fsgd_input.mgh created? What do you get when you run:
mri_info fsgd_input.mgh

On 10/14/10 7:53 PM, Pradeep wrote:

Hello All,

I get the following error while running mri_glmfit. I am using 
freesurfer V5.0. But qdce seem to run well with the similar settings.


-log---

[pthiyyagura@ fsgd]$ mri_glmfit --glmdir g2v0 --y fsgd_input.mgh 
--fsgd g2v0.fsgd --C group.diff.mtx

gdfReadHeader: reading g2v0.fsgd
INFO: gd2mtx_method is dods

$Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve Exp $
cwd /data/rawdata/API/FS_MPRAGE/fsgd
cmdline mri_glmfit --glmdir g2v0 --y fsgd_input.mgh --fsgd g2v0.fsgd 
--C group.diff.mtx

sysname  Linux
hostname
machine  x86_64
user pthiyyagura
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y/data/rawdata/API/FS_MPRAGE/fsgd/fsgd_input.mgh
logyflag 0
usedti  0
FSGD g2v0.fsgd
glmdir g2v0
IllCondOK 0
DoFFx 0
Creating output directory g2v0
Loading y from /data/rawdata/API/FS_MPRAGE/fsgd/fsgd_input.mgh
MRIalloc: could not allocate 1378828612 slices

Cannot allocate memory

end---

Any suggestion on this would be greatly appreciated.

Thanks,
Pradeep


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[Freesurfer] Cannot allocate memory

[Pradeep]

Hello All,

I get the following error while running mri_glmfit. I am using freesurfer
V5.0. But qdce seem to run well with the similar settings.

-log---

[pthiyyagura@ fsgd]$ mri_glmfit --glmdir g2v0 --y fsgd_input.mgh --fsgd
g2v0.fsgd --C group.diff.mtx
gdfReadHeader: reading g2v0.fsgd
INFO: gd2mtx_method is dods

$Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve Exp $
cwd /data/rawdata/API/FS_MPRAGE/fsgd
cmdline mri_glmfit --glmdir g2v0 --y fsgd_input.mgh --fsgd g2v0.fsgd --C
group.diff.mtx
sysname  Linux
hostname
machine  x86_64
user pthiyyagura
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y/data/rawdata/API/FS_MPRAGE/fsgd/fsgd_input.mgh
logyflag 0
usedti  0
FSGD g2v0.fsgd
glmdir g2v0
IllCondOK 0
DoFFx 0
Creating output directory g2v0
Loading y from /data/rawdata/API/FS_MPRAGE/fsgd/fsgd_input.mgh
MRIalloc: could not allocate 1378828612 slices

Cannot allocate memory

end---

Any suggestion on this would be greatly appreciated.

Thanks,
Pradeep
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[Freesurfer] ERROR: mpr2mni305 failed

[Maria Luisa Mandelli]

Hi!

I get this error running recon_all


Applications/freesurfer/bin/talairach_avi --i nu.mgz --xfm
transforms/talairach.auto.xfm
ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

parameter  1  1.219086 -> -0.50 qaram1.5209
imgrege: no voxels in register
ERROR: 'imgreg_4dfp
/data/henry4/Applications/freesurfer/average/711-2C_as_mni_average_305
/data/henry4/Applications/freesurfer/average/711-2B_as_mni_average_305_mask
talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed!
status=254
ERROR: mpr2mni305 execution aborted

Have someone some ideas about this error?

thank you!
-- 
Maria Luisa Mandelli

Postdoctoral Fellow
Center for Functional and Molecular Imaging
UCSF Department of Radiology and Biomedical Imaging
China Basin Landing
185 Berry Street, Suite 350
San Francisco, CA 94107
phone (415) 353-9419
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Re: [Freesurfer] MNI152

[Douglas N Greve]

Here are some instructions. I have not tested them myself, so make sure 
you check the registrations along the way.

doug



1. Register functional (template.nii) to anatomical matrix (may
   already be done in fsfast)

bbregister --s $subject --bold --init-fsl \
   --mov template.nii --reg register.dof6.dat

2. Register anatomical to mni152:
  mni152reg --s $subject
   Creates $SUBJECTS_DIR/$subject/mri/transforms/reg.mni152.2mm.dat

3. Check registration
   tkregister2 --mov $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \
 --reg $SUBJECTS_DIR/$subject/mri/transforms/reg.mni152.2mm.dat

4. Create registration between functional and mni152
  mri_matrix_multiply -im register.dof6.dat \
   -iim reg.mni152.2mm.dat -om reg.mni152.dat

5. Check registration
 tkregister2 --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \
   --mov template.nii --reg reg.mni152.dat

6. Resample func to mni152 space
 mri_vol2vol --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \
   --mov template.nii --reg reg.mni152.dat --o template.mni152.nii



Yigal Agam wrote:
> Hi,
>
> Is it possible to export a functional volume from individual brain space 
> to mni152, so it can be overlaid on the standard mni152 brain in fslview?
>
> Thanks,
> Yigal
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MGH-NMR Center
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Fax: 617-726-7422

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Re: [Freesurfer] Problem with intensity normalization

[Douglas N Greve]

Jing, why are you running these commands by hand instead of just running 
recon-all? These are very complicated steps and don't lend themselves to 
running by hand.

doug

Huo, Jing wrote:
> Hi,
>
> I have a problem with using mri_normalize for intensity normalization for 
> T1w+contrast 3D volumes.
>
> What I ran:
> mri_convert t1.hdr t1.mgz
> mri_normalize -g 1 t1.mgz t1_norm.mgz
> mri_convert t1_norm.mgz t1_norm.hdr
>
> (1) The first problem is that all volumes are 256*256*256 as output. Why are 
> there dummy slices? Is there an automatic way to get rid of the dummy slices?
>
> (2) For 1/3 of the 50 cases, I observed a spatial shift for some voxels. I 
> was wondering whether this comes from the spatial registration, but it is 
> wierd coz the rest 2/3 of the cases are pretty OK visually. Anyone has 
> similar experience before? That would be very helpful. Thanks.
>
> (3) For 4 cases, the brain white matter was normalized to 59 instead of 110. 
> I dunno why...
>
> Thanks! I will really appreciate if anyone could  help here!
>
> Best,
> Jing
>
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> Unauthorized redisclosure or failure to maintain confidentiality may subject 
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] Problem with intensity normalization

[Huo, Jing]

Hi,

I have a problem with using mri_normalize for intensity normalization for 
T1w+contrast 3D volumes.

What I ran:
mri_convert t1.hdr t1.mgz
mri_normalize -g 1 t1.mgz t1_norm.mgz
mri_convert t1_norm.mgz t1_norm.hdr

(1) The first problem is that all volumes are 256*256*256 as output. Why are 
there dummy slices? Is there an automatic way to get rid of the dummy slices?

(2) For 1/3 of the 50 cases, I observed a spatial shift for some voxels. I was 
wondering whether this comes from the spatial registration, but it is wierd coz 
the rest 2/3 of the cases are pretty OK visually. Anyone has similar experience 
before? That would be very helpful. Thanks.

(3) For 4 cases, the brain white matter was normalized to 59 instead of 110. I 
dunno why...

Thanks! I will really appreciate if anyone could  help here!

Best,
Jing

IMPORTANT WARNING:  This email (and any attachments) is only intended for the 
use of the person or entity to which it is addressed, and may contain 
information that is privileged and confidential.  You, the recipient, are 
obligated to maintain it in a safe, secure and confidential manner.  
Unauthorized redisclosure or failure to maintain confidentiality may subject 
you to federal and state penalties. If you are not the intended recipient, 
please immediately notify us by return email, and delete this message from your 
computer.

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Re: [Freesurfer] FDR in gray matter

[Douglas N Greve]

There is currently not a way to mask for anything but the brain. I just 
found out that that did not work (and never had). That has been fixed. I 
also added the ability to specify an FDR mask using an environment 
variable, like

setenv TKM_FDR_MASK yourfdrmask.mgz

This will look in the $SUBJECTS_DIR for subject/mri/yourfdrmask.mgz. 
Note that you must check the "mask to brain"  option next to the FDR 
button.

This two changes will be live in both dev and stable upon the next update.

You can make the mask you want from aparc+aseg.mgz using mri_binarize 
with the --match option to choose the structures you want to include in 
the mask.

doug


Yigal Agam wrote:
> Hi,
>
> Is it possible to restrict FDR correction to gray matter in tkmedit?
>
> Thanks
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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] Retinotopic mapping of only polar data]

[Douglas N Greve]

Hi Frank, sfa-sess does not exist in  version 5 of FreeSurfer because 
its functions have been incorporated into selxavg3-sess. It will be a 
lot easier to support you if you move to version 5. Unfortunately, I 
have been slow in getting it documented. Having said that, I think the 
new version is a lot easier to use. It is very similar to regular task 
studies, which is pretty well documented (see 
http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt).

For retinotopy, there are only a few deviations:
1.a. When you create the analysis, specify something like:
mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -fwhm 5  
-retinotopy 30 -paradigm rtopy.par
   where "-retinotopy 30" means that it is a retinotopy study with a 
period of 30 sec
1.b Run selxavg3-sess (instead of sfa-sess)
1.c Run tksurfer-sess, like
tksurfer-sess -s sess -a rtopy.self.lh
  This will show you the eccen and polor contrasts
2.a Create a field sign (with an occipital patch) with:
fieldsign-sess -a rtopy.lh -s sess -occip
2.b View the fieldsign
tksurfer-sess -s sess -a rtopy.self.lh -fieldsign

The above assumes that you want to analyze the data on the subject's 
left hemi. Make and run anther analysis for the right hemi

doug


f.le...@donders.ru.nl wrote:
> Hi everyone,
>
> The e-mail included below I sent some time ago, maybe it slipped through. In 
> the mean time I did find out I can plot the results with tksurfer-sess like
>
> tksurfer-sess -s S2_FS -h rh -analysis rtopy -c polar -map h
>
> But then two big questions remain:
> - How to interpret these color codes?
> - How to threshold them on significance?
> (Third one: how to interpolate them to get away from the patchy 
> representation?)
>
> The other questions stated below are also still relevant.
>
> Asked this before, but can we add stuff ourselves to the wiki? Found out 
> quite a bit about the retinotopic inner workings which I wasn't able to find 
> anywhere else, might help some others.
>
> kind regards,
>
>  Frank
>
> Old topic, but it is directly related, so I'll just continue it here.
>
> In the end I have the spots on the right place, but now it's not clear
> to me how to interpret the map. I have created three overlays (sign,
> log10 * sin, log10 * cos, like mentioned in selfreq.pdf) and loaded them
> all three in tksurfer. Most important question now: how to relate these
> three to get one figure instead of three separate?
>
> Other more minor questions:
> - What do the values actually mean? Apparently I can threshold on the
> basis of them, but that does't make sense to do, because the direction
> info is also in there, right? I should probably threshold the F-values
> first, before overlaying them on the inflated brain.
> - What happened to sfa-sess in the new version of freesurfer? I can't
> seem to find it.
> - Why does the sfa-sess script check whether amp data is present?
> Looking at the script, the line that checks whether there is amplitude
> data can safely be removed.
> - Just like the original Sereno paper, I have 20s pre and post stimulus
> presentation time. I now only use the data where the convolved DM
> predicts there will be signal, so discarding the first 20s and, due to
> the HRF, keeping almost the entire second 20s. Is this the correct thing
> to do, or should I rather keep everything / make sure I have an exact
> number of periods for each stimulus?
>
> Thanks a lot in advance,
>
>kind regards,
>
>  Frank
>
>
> On Mon, 2010-01-18 at 17:32 -0500, Douglas N Greve wrote:
>   
>> If the activation is showing up in the wrong places, then that probably 
>> means that the registration is off. Have you checked the registration.
>>
>> doug
>>
>> f.le...@donders.ru.nl wrote:
>> 
>>> Probably my e-mail just slipped through, so just a short notice that I 
>>> still have the problem with the overlay mentioned in the last e-mail:
>>>
>>> "I now have a polar map overlayed on my inflated brain. But something seems 
>>> to be amiss, because it plots it mainly on the temporal lobe, with nothing 
>>> on the most dorsal slices, while actually I only scanned the 18 most dorsal 
>>> (oriented along the occipital-parietal axis), sot here shouldn't be 
>>> anything in the temporal or inferior frontal lobe. How can this be/where is 
>>> it going wrong?
>>>
>>> Moreover, I'm not sure on the format used by the polar map: the scale bar 
>>> states it ranges from 1.18 to 1.18, but I don't see the sense in that. What 
>>> will come out? Radians I pressume?"
>>>
>>> Is it possible to edit the wikipages ourselves btw? I could add some more / 
>>> update the info on the retinotopic mapping to help other people when I got 
>>> it all figured out.
>>>
>>>kind regards, thanks in advance,
>>>
>>> Frank
>>>
>>> - Original Message -
>>> From: "f.le...@donders.ru.nl" 
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Sent: Monday, January 11, 2010 9:15:43 AM GMT +01:00 Amsterdam / Berlin / 
>>> Bern

[Freesurfer] postdoctoral fellow position for dementia research

[Anqi Qiu]

Postdoctoral Fellow Position on Dementia NeuroImaging
Job description:
National University of Singapore (NUS) is a leading global university
centred in Asia. It offers a global approach to education and research,
with a focus on Asian perspectives and expertise. Computation functional
anatomy laboratory at NUS (http://www.bioeng.nus.edu.sg/cfa) focuses on
brain and cognition studies using neuroimaging techniques. Our group is
leading the dementia neuroimaging project in Singapore. The project
involves multi-modal MRI techniques, including resting fMRI, HARDI, and
ASL. We are looking for a research fellow who is interested in multi-modal
MRI studies in dementia, especially, who is interested in developing
anatomical and functional connectivity methods or investigating anatomical
and functional connectivity in dementia. We offer high salary with medical
and other benefits.

Requirements:
•   Ph. D or MD
•   Background on Alzheimer’s disease or vascular disease research is
preferable but necessary
•   Knowledge in statistical analysis is necessary
•   Good communication and writing skills in English language



If you are interested in the jobs listed below, please send your CV to
Dr.  Anqi QIU
Division of Bioengineering
National University of Singapore
Email: bi...@nus.edu.sg
Phone: +(65) 6516 7002

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[Freesurfer] postdoctoral fellow position for dementia research

[Anqi Qiu]

Postdoctoral Fellow Position on Dementia NeuroImaging
Job description:
National University of Singapore (NUS) is a leading global university
centred in Asia. It offers a global approach to education and research,
with a focus on Asian perspectives and expertise. Computation functional
anatomy laboratory at NUS (http://www.bioeng.nus.edu.sg/cfa) focuses on
brain and cognition studies using neuroimaging techniques. Our group is
leading the dementia neuroimaging project in Singapore. The project
involves multi-modal MRI techniques, including resting fMRI, HARDI, and
ASL. We are looking for a research fellow who is interested in multi-modal
MRI studies in dementia, especially, who is interested in developing
anatomical and functional connectivity methods or investigating anatomical
and functional connectivity in dementia. We offer high salary with medical
and other benefits.

Requirements:
•   Ph. D or MD
•   Background on Alzheimer’s disease or vascular disease research is
preferable but necessary
•   Knowledge in statistical analysis is necessary
•   Good communication and writing skills in English language



If you are interested in the jobs listed below, please send your CV to
Dr.  Anqi QIU
Division of Bioengineering
National University of Singapore
Email: bi...@nus.edu.sg
Phone: +(65) 6516 7002

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[Freesurfer] FDR in gray matter

[Yigal Agam]

Hi,

Is it possible to restrict FDR correction to gray matter in tkmedit?

Thanks
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Re: [Freesurfer] Fwd: Mapping labels to the RH on Macs

[Nick Schmansky]

a new qdec, which fixes the rh hemi problem found by Tessa and Derin
described below, is available for download from here:

http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/

for the mac, goto the macos-leopard-intel/  dir, for 64b linux, goto
linux-centos4_x86_64/ 

copy the file qdec.bin to your $FREESURFER_HOME/bin dir, then type:

chmod a+x $FREESURFER_HOME/bin/qdec.bin

the fix adds code to look for "rh." or "lh." in the surface file name
when loaded and sets an interval variable appropriately.

n.

On Wed, 2010-10-13 at 18:22 -0400, Nick Schmansky wrote:
> I see the problem now.  I'll try to have a fixed verson of qdec posted
> tomorrow.
> 
> n.
> 
> On Wed, 2010-10-13 at 16:32 -0500, Tessa Harrison wrote:
> > Yes, I see what you mean. We did think of that back when we were first
> > troubleshooting, and simply changing the option to rh on the Design
> > tab did not solve the problem (I just checked again and it still
> > points to lh). So it looks like unless you actually run an analysis
> > from the design tab, the 'Map to All Subjects' option points to the
> > lh. Thank you for helping us solve this problem! 
> > 
> > 
> > -Tessa
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > On Wed, Oct 13, 2010 at 4:10 PM, Nick Schmansky
> >  wrote:
> > When working with a manually loaded surface, and a new rh
> > label is drawn
> > or a prior one loaded, prior to pressing the 'Map to All
> > Subjects
> > Option', do you switch the hemi menu selection in the Design
> > tab to
> > 'rh'?  I'm guessing not, because it is not evident that you
> > would need
> > to do this, but it explains the problem you are seeing.  In my
> > own past
> > usage of qdec, I havent run the use case you described, so
> > until now I
> > didnt anticipate this problem.  The problem is that when
> > loading a
> > surface or label, there is no step or pop-up box or mechanism
> > to tell
> > qdec which surface it is loading.  I suppose it could infer it
> > from the
> > name (parse-out 'rh' or 'lh), but that is kind of hacky.  What
> > I need to
> > add is a pop-up box or some user interface gate that forces
> > the user to
> > set the hemisphere.  Otherwise, qdec just default to 'lh'.  So
> > until
> > that feature is added, you will just have to remember to goto
> > the Design
> > tab and set the hemi to whatever was loaded.
> > 
> > n.
> > 
> > 
> > 
> > 
> > On Wed, 2010-10-13 at 14:22 -0500, Tessa Harrison wrote:
> > > Nick,
> > >
> > >
> > > Thanks for getting back to me.   After you said you could
> > not
> > > replicate the problem, we went back in and reexamined.  It
> > seems that
> > > if you draw a new rh label or pull up a previously created
> > rh label in
> > > qdec on a loaded surface (i.e., rh.pial, etc), the “Map to
> > All
> > > Subjects” option points to the lh (as seen in Derin’s
> > output).
> > >
> > >
> > >
> > > We tried mapping rh labels after loading them onto an rh
> > analysis and
> > > it works just fine, which may have been why you could not
> > replicate
> > > our issue?
> > >
> > >
> > >
> > > We were using the load surface option so as to save time by
> > avoiding
> > > running an analysis every time we wanted to map a label
> > created with
> > > tksurfer to new subjects. Regardless, I am happy to know
> > there is a
> > > work-around for this issue!
> > >
> > >
> > >
> > > -Tessa
> > >
> > >
> > >
> > >
> > >
> > > On Mon, Oct 11, 2010 at 9:18 PM, Nick Schmansky
> > >  wrote:
> > > Tessa and Derin,
> > >
> > > I'm unable to replicate this problem in the mac or
> > on linux,
> > > using v5.0.
> > > I'm running a group analysis on the rh, then drawing
> > a lable
> > > and
> > > selecting the Map Label to Subject option, and the
> > label2label
> > > command
> > > uses 'rh' as the --hemi option for me.
> > >
> > > Can you describe your usage so that I can replicate
> > the
> > > problem?
> > >
> > > n.
> > >
> > >
> > > On Mon, 2010-10-11 at 10:26 -0500, Derin Cobia
> > wrote:
> > > > I'm experiencing this as well on my Mac OS X
> > distribution of
> > > FS
> > > > v5.0.0.  Here is 

Re: [Freesurfer] converting IMA files

[Douglas N Greve]

Lisa, does the output directory exist and do you have write permissions? 
Can you convert it to some other format (eg, mgz)?

doug

Lisa F. Akiyama wrote:
> Any suggestions?
>
>
> Best,
> Lisa
>  __
>
>
>
> On Fri, Oct 8, 2010 at 11:14 AM, Lisa F. Akiyama  > wrote:
>
> Hi Doug,
>
> I have plenty of disk space available.
> I am currently
> running freesurfer-Darwin-leopard-ppc-stable-pub-v5.0.0.
>
>
> Best,
> Lisa
>
>
>
>
>
> On Fri, Oct 8, 2010 at 11:10 AM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Are you running out of disk space? What version of FS are you
> using?
>
> doug
>
> Lisa F. Akiyama wrote:
>
> Hello,
>
> I am a Freesurfer newbie trying to use the mri_convert
> command to convert IMA format files to either nii or
> nifti1 format files.
> Whenever I run the command I get an error at the very end
> saying that it failed to write (please see below for the
> exact output error that was displayed).
> Any help would be greatly appreciated.
> Thank you in advance.
>
>
> Best,
> Lisa Akiyama
>
>
>% mri_convert -i $SUBJ_DIR/393-2-4.ima -ot nii -o
> 393-2-4.nii
>
>mri_convert -i
>/Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima
> -ot nii -o
>393-2-4.nii
>$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50
> greve Exp $
>
>reading from
> /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima...
>
>rows = 256
>
>cols = 256
>
>TR=11.40, TE=4.40, TI=300.00, flip angle=15.00
>
>i_ras = (-0, -1, -0)
>
>j_ras = (-0, 0, -1)
>
>k_ras = (-1, 0, 0)
>
>writing to 393-2-4.nii...
>
>niiWrite(): error opening file 393-2-4.nii
>
>ERROR: failure writing 393-2-4.nii as volume type 24
>
>
>
>% mri_convert -i $SUBJ_DIR/393-2-4.ima -ot nifti1 -o
> 393-2-4
>
>mri_convert -i
>/Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima
> -ot nifti1 -o
>393-2-4
>$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50
> greve Exp $
>
>reading from
> /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima...
>
>rows = 256
>
>cols = 256
>
>TR=11.40, TE=4.40, TI=300.00, flip angle=15.00
>
>i_ras = (-0, -1, -0)
>
>j_ras = (-0, 0, -1)
>
>k_ras = (-1, 0, 0)
>
>writing to 393-2-4...
>
>nifti1Write(): error opening file 393-2-4.hdr
>
>ERROR: failure writing 393-2-4 as volume type 20
>
>
>
> 
> 
>
> ___
> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
>
>
>
> 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.
>
>
>

-- 
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] converting IMA files

[Lisa F. Akiyama]

Any suggestions?


Best,
Lisa
 __



On Fri, Oct 8, 2010 at 11:14 AM, Lisa F. Akiyama  wrote:

> Hi Doug,
>
> I have plenty of disk space available.
> I am currently running freesurfer-Darwin-leopard-ppc-stable-pub-v5.0.0.
>
>
> Best,
> Lisa
>
>
>
>
>
> On Fri, Oct 8, 2010 at 11:10 AM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> Are you running out of disk space? What version of FS are you using?
>>
>> doug
>>
>> Lisa F. Akiyama wrote:
>>
>>> Hello,
>>>
>>> I am a Freesurfer newbie trying to use the mri_convert command to convert
>>> IMA format files to either nii or nifti1 format files.
>>> Whenever I run the command I get an error at the very end saying that it
>>> failed to write (please see below for the exact output error that was
>>> displayed).
>>> Any help would be greatly appreciated.
>>> Thank you in advance.
>>>
>>>
>>> Best,
>>> Lisa Akiyama
>>>
>>>
>>>% mri_convert -i $SUBJ_DIR/393-2-4.ima -ot nii -o 393-2-4.nii
>>>
>>>mri_convert -i
>>>/Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima -ot nii -o
>>>393-2-4.nii
>>>$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
>>>
>>>reading from /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima...
>>>
>>>rows = 256
>>>
>>>cols = 256
>>>
>>>TR=11.40, TE=4.40, TI=300.00, flip angle=15.00
>>>
>>>i_ras = (-0, -1, -0)
>>>
>>>j_ras = (-0, 0, -1)
>>>
>>>k_ras = (-1, 0, 0)
>>>
>>>writing to 393-2-4.nii...
>>>
>>>niiWrite(): error opening file 393-2-4.nii
>>>
>>>ERROR: failure writing 393-2-4.nii as volume type 24
>>>
>>>
>>>
>>>% mri_convert -i $SUBJ_DIR/393-2-4.ima -ot nifti1 -o 393-2-4
>>>
>>>mri_convert -i
>>>/Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima -ot nifti1 -o
>>>393-2-4
>>>$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
>>>
>>>reading from /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima...
>>>
>>>rows = 256
>>>
>>>cols = 256
>>>
>>>TR=11.40, TE=4.40, TI=300.00, flip angle=15.00
>>>
>>>i_ras = (-0, -1, -0)
>>>
>>>j_ras = (-0, 0, -1)
>>>
>>>k_ras = (-1, 0, 0)
>>>
>>>writing to 393-2-4...
>>>
>>>nifti1Write(): error opening file 393-2-4.hdr
>>>
>>>ERROR: failure writing 393-2-4 as volume type 20
>>>
>>>
>>>
>>> 
>>>
>>> ___
>>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>
>>
>>
>> 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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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.

Re: [Freesurfer] Retinotopic mapping of only polar data]

[f.le...@donders.ru.nl]

Hi everyone,

The e-mail included below I sent some time ago, maybe it slipped through. In 
the mean time I did find out I can plot the results with tksurfer-sess like

tksurfer-sess -s S2_FS -h rh -analysis rtopy -c polar -map h

But then two big questions remain:
- How to interpret these color codes?
- How to threshold them on significance?
(Third one: how to interpolate them to get away from the patchy representation?)

The other questions stated below are also still relevant.

Asked this before, but can we add stuff ourselves to the wiki? Found out quite 
a bit about the retinotopic inner workings which I wasn't able to find anywhere 
else, might help some others.

kind regards,

 Frank

Old topic, but it is directly related, so I'll just continue it here.

In the end I have the spots on the right place, but now it's not clear
to me how to interpret the map. I have created three overlays (sign,
log10 * sin, log10 * cos, like mentioned in selfreq.pdf) and loaded them
all three in tksurfer. Most important question now: how to relate these
three to get one figure instead of three separate?

Other more minor questions:
- What do the values actually mean? Apparently I can threshold on the
basis of them, but that does't make sense to do, because the direction
info is also in there, right? I should probably threshold the F-values
first, before overlaying them on the inflated brain.
- What happened to sfa-sess in the new version of freesurfer? I can't
seem to find it.
- Why does the sfa-sess script check whether amp data is present?
Looking at the script, the line that checks whether there is amplitude
data can safely be removed.
- Just like the original Sereno paper, I have 20s pre and post stimulus
presentation time. I now only use the data where the convolved DM
predicts there will be signal, so discarding the first 20s and, due to
the HRF, keeping almost the entire second 20s. Is this the correct thing
to do, or should I rather keep everything / make sure I have an exact
number of periods for each stimulus?

Thanks a lot in advance,

   kind regards,

 Frank


On Mon, 2010-01-18 at 17:32 -0500, Douglas N Greve wrote:
> If the activation is showing up in the wrong places, then that probably 
> means that the registration is off. Have you checked the registration.
> 
> doug
> 
> f.le...@donders.ru.nl wrote:
> > Probably my e-mail just slipped through, so just a short notice that I 
> > still have the problem with the overlay mentioned in the last e-mail:
> >
> > "I now have a polar map overlayed on my inflated brain. But something seems 
> > to be amiss, because it plots it mainly on the temporal lobe, with nothing 
> > on the most dorsal slices, while actually I only scanned the 18 most dorsal 
> > (oriented along the occipital-parietal axis), sot here shouldn't be 
> > anything in the temporal or inferior frontal lobe. How can this be/where is 
> > it going wrong?
> >
> > Moreover, I'm not sure on the format used by the polar map: the scale bar 
> > states it ranges from 1.18 to 1.18, but I don't see the sense in that. What 
> > will come out? Radians I pressume?"
> >
> > Is it possible to edit the wikipages ourselves btw? I could add some more / 
> > update the info on the retinotopic mapping to help other people when I got 
> > it all figured out.
> >
> >kind regards, thanks in advance,
> >
> > Frank
> >
> > - Original Message -
> > From: "f.le...@donders.ru.nl" 
> > To: freesurfer@nmr.mgh.harvard.edu
> > Sent: Monday, January 11, 2010 9:15:43 AM GMT +01:00 Amsterdam / Berlin / 
> > Bern / Rome / Stockholm / Vienna
> > Subject: Re: [Freesurfer] Retinotopic mapping of only polar data
> >
> > Hi everyone,
> >
> > Doug: thanks a lot for the reply, that indeed worked, I now have a polar 
> > map overlayed on my inflated brain. But something seems to be amiss, 
> > because it plots it mainly on the temporal lobe, with nothing on the most 
> > dorsal slices, while actually I only scanned the 18 most dorsal (oriented 
> > along the occipital-parietal axis), sot here shouldn't be anything in the 
> > temporal or inferior frontal lobe. How can this be/where is it going wrong?
> >
> > Moreover, I'm not sure on the format used by the polar map: the scale bar 
> > states it ranges from 1.18 to 1.18, but I don't see the sense in that. What 
> > will come out? Radians I pressume?
> >
> > kind regards, thanks a lot in advance,
> >
> >   Frank
> >
> > - Original Message -
> > From: "Douglas N Greve" 
> > To: "Frank Leoné" 
> > Cc: freesurfer@nmr.mgh.harvard.edu
> > Sent: Friday, January 8, 2010 4:26:21 PM GMT +01:00 Amsterdam / Berlin / 
> > Bern / Rome / Stockholm / Vienna
> > Subject: Re: [Freesurfer] Retinotopic mapping of only polar data
> >
> > You can generate a register.dat with either fslregister-sess or 
> > spmregister-sess, or, if you have it in your version, use bbregister 
> > (note that there is not a -sess version for this yet).
> >
> > Y