[Freesurfer] Conversion niifty to dcm

[stdp82]

Hi list,
there is a way to convert niifty or .par/.rec in DICOM?
Thank you very much,

Stefano   ___
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Re: [Freesurfer] blood hyper-intensity

[Sebastian Moeller]

Hi Colin,


On Oct 24, 2013, at 00:24 , Colin Reveley  wrote:

> Hi - 
> 
> I wonder if anyone has experience in dealing with T1 images where there is 
> hyperintenisty of blood vessels?

This looks like receive & transmit surface coil data to me. For 
MPRAGEs, in my experience, switching to receive only surface coil (and assuming 
a whole body scanner) and the body coil for transmit will darken the the blood 
vessels again. Or you could use 8mb/kg bodyweight feraheme to reduce the blood 
signal as well. Both methods will obviously not work retrospectively. I have no 
experience with MDEFT, so the fereheme might not work. (But if you go that 
route: feraheme is an excellent functional contrast agent in NHPs for EPIs)


> 
> the data involved is MDEFT scans where only a head coil is used. I read it is 
> a long solved problem for acquisition, but these scans do not correct it and 
> nor will future scans.
> 
> the difficulty is getting 3 classes (CSF,WM,GM) for nu_correct,mri_normalise 
> or FSL Fast or whatever.
> 
> It's quite a big obstacle for data that is otherwise quite excellent. 
> 
> One would think one could just threshold it out after brain extraction and to 
> an extent one can but it's very imperfect. segmenting 4 classes doesn't 
> especially work either (so far)
> 
> if anyone has experience segmenting this stuff (especially getting 
> mri_normalise to work) I'd be grateful for advice.

How does it affect mri_normalize? I typically used:
mri_normalize -n 1 -no1d -gentle ${src_dir}/${src_vol} ${targ_dir}/${targ_vol} 
-v -mprage
on NHPs and:
mri_normalize -f ${controlpoints} ${mri_normalize_options_string} -MASK 
${src_dir}/${mask} ${src_dir}/${in_vol} ${targ_dir}/${unmasked_brain} -mprage
for control point based normalization (which does not look required for your 
nice data)
I guess for MDEFT I would skip -mprage.

I hope that helps at least some.

best
Sebastian

> 
> e.g. attached
> 
> Colin Reveley
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[Freesurfer] improvement of segmentation qualitiy by setting control points

[Annemarie Brandhofe]

Dear freesurfer community,

we have encountered some problems with setting control points to improve
segmentation quality. Mainly, white matter was classified as grey matter
after completion of the first run that incorporated control points. Now we
have several questions, we would be very thankful for your comments:

1. According to your expereince, how many control points for the overall
brain are usually necessary to obtain good segmentation results?

2. Are control points necessary at all? Is there a way to control the
segmentation quality?

3. Is there any visual example on how to best set control points?

Thank you for your help,

Annemarie
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Re: [Freesurfer] installation trouble - error message subjects directory not recognised

[Z K]

Hi Sven,

Whats most likely happening is that you are defining SUBJECTS_DIR prior 
to sourcing SetUpFreeSurfer.csh. Freesurfer will not overwrite the 
SUBJECTS_DIR environment variable if it already exists at the time of 
sourcing the SetUpFreeSurfer.csh. This is most likely occuring in your 
.cshrc file.

To verify, type 'echo $SUBJECTS_DIR' before sourcing and see what the 
output says.

-Zeke

On 10/24/2013 09:10 AM, muellersvenc wrote:
> Hi all,
>
> I am running into trouble testing my freesurfer installation on a Mac 
> (10.6.8). I followed all steps in the guide but there is something funny that 
> freesurfer does not seem to recognise its own "subjects" directory (see 
> attached screenshot). If screenshot is not visible, it says:
>
>  freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> WARNING: Applications/freesurfer/subjects does not exist
> FREESURFER_HOME   /Applications/freesurfer
> FSFAST_HOME   /Applications/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  Applications/freesurfer/subjects
> MNI_DIR   /Applications/freesurfer/mni
> FSL_DIR   /usr/local/fsl
>
> I think it might have to do with the fact that there is a "/" missing in 
> front of the "Applications" but I don't know where/how to change this. I 
> checked my StartUp.csh file and there everything seems fine. However, the 
> subjects directory was definitely created by freesurfer (also screenshot) so 
> there is a mismatch somewhere.
>
> I am sure it is a simple thing but can someone please let me know what I 
> should do so I can start to enjoy freesurfer?
>
> Many thanks in advance,
>
> sven
>
>
>
>
> ___
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>
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[Freesurfer] Volumes in native or normalized space, and eTIV

[Dorian P.]

Dear all,

Excuse if these are simple questions but I am a bit confused on the
significance of the volume measures.

1. Are the volumes of ROIs calculated after normalization?

2. If volumes are calculated post-normalization, why is correction for eTIV
needed?

3. What is the quickest way to correct for eTIV?

Thank you.
Dorian
TJU
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Re: [Freesurfer] TRACULA statistics

[Anastasia Yendiki]

No, the last 3 columns (Min Max Range) are the minimum, maximum, and range 
(maximum - minimum) or the values in path.pd.nii.gz.


But it does look like mri_segstats can get you what you want, if you use a 
binarized version of path.pd.nii.gz. Use mri_binarize (possibly with a 
threshold, if you want to threshold the distribution) on path.pd.nii.gz, 
which will give you an output volume that has 1 inside and 0 outside the 
pathway. Then you run mri_segstats on that binarized volume. What you want 
(the volume of the pathway inside each structure) will be the sum of the 
1's of the pathway inside each structure. Because mri_segstats doesn't 
give you the sum but it does give you the mean, you'll have to calculate 
the sum as the mean multiplied by the total number of voxels in the same 
structure. So column "Mean" multiplied by column "NVoxels" will give you 
the number of voxels in each structure that intersect the pathway.


On Thu, 24 Oct 2013, Lucia Billeci wrote:


Dear Anastasia,
yes I was referring to the last three columns. So for the last three columns
is it right what I told you? Is it the volume of the path? 

Lucia

Lucia

_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

Dr. Lucia Billeci, PhD
Institute of Clinical Physiology (IFC)
National Research Council (CNR)
via Moruzzi 1, 56124, Pisa
ITALY
Tel: +39-0506213204
e-mail: lucia.bill...@ifc.cnr.it
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 




Il giorno 23/ott/2013, alle ore 19:24, Anastasia Yendiki ha scritto:


  Hi Lucia - The columns "NVoxels Volume_mm3" in the mri_segstats
  output are the volumes of each of the structures in the
  aparc+aseg, so those columns have nothing to do with the path.
  The last few columns, "Mean StdDev Min Max Range", are related
  to the values in path.pd.nii.gz.

  Hope this helps,
  a.y

  On Wed, 23 Oct 2013, Lucia Billeci wrote:

Dear Anastasia,


I tried the command you suggested me and i obtained
the output I attach to the mail.


I would like to ask you if I understood well shot it
means. In this case left uncinatus connects the
following cortex areas:


ctx-lh-fusiform

ctx-lh-inferiortemporal

ctx-lh-lateralorbitofrontal

ctx-lh-medialorbitofrontal

ctx-lh-middletemporal

ctx-lh-rostralanteriorcingulate

ctx-lh-superiortemporal

ctx-lh-temporalpole

ctx-lh-insula


and for each area I have the volume of the path. Is
it correct?


Thanks

Lucia







_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _


Dr. Lucia Billeci, PhD

Institute of Clinical Physiology (IFC)

National Research Council (CNR)

via Moruzzi 1, 56124, Pisa

ITALY

Tel: +39-0506213204

e-mail: lucia.bill...@ifc.cnr.it

_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _





Il giorno 18/ott/2013, alle ore 17:32, Anastasia
Yendiki ha scritto:



  Hi Lucia - You can probably do that with
  mri_segstats. Try something like:


  mri_segstats --seg
  dlabel/diff/aparc+aseg.bbr.nii.gz --ctab
  $FREESURFER_HOME/FreeSurferColorLUT.txt
  --excludeid 0 --sum output.txt --i
  dpath/lh.unc_AS_avg32_mni_flt/path.pd.nii.gz


  And similarly for any other pathway. See
  the mri_segstats help for more usage
  info. Let me know if this gives you what
  you need.


  a.y


  On Fri, 18 Oct 2013, Lucia Billeci
  wrote:


Thanks Anastasia, this is
useful for visualization.
But to construct a table

with for each tracts the
parcellation regions that it
connects do I need to

look at the image?

Lucia

On Oct 18, 2013, at 3:48 PM,
Anastasia Yendiki wrote:


Hi Lucia - You can look
at the tracula output over
the cortical

parcellation and
subcortical segmentation in
the individual's

diffusion space like
this:


freeview
dmri/dtifit_FA.nii.gz


dlabel/diff/aparc+aseg.bbr.nii.gz:colormap=lut:opacity=.5
-tv

dpath/merged_avg33_mni_bbr.mgz


Hope this helps,

   

Re: [Freesurfer] installation trouble - error message subjects directory not recognised

[muellersvenc]

Hi Zeke,

that seems to have worked (strangely because I didn't really do anything 
different before other than a fresh reinstall).

However, now I have problems with the license file when trying to test the 
installation as suggested on the "Testing your freesurfer installation" 
webpage. 

I did a fresh installation, then created a ".license" file using the text 
editor containing the three lines that were sent to me by email and placed this 
file into the freesurfer folder which is my FREESURFER_HOME 
(/Applications/freesurfer). Then I did the sourcing. And then when I type for 
instance 

[pp05c332:/Applications] switch% tkmedit bert orig.mgz
--
ERROR: FreeSurfer license file /Applications/freesurfer/.license not found.
  If you are outside the NMR-Martinos Center,
  go to http://surfer.nmr.mgh.harvard.edu to 
  get a valid license file (it's free).
  If you are inside the NMR-Martinos Center,
  make sure to source the standard environment.
--
[pp05c332:/Applications] switch% 


Any ideas what I am doing wrong? I changed the settings on my computer a while 
ago and I can see the hidden files so can also see that there is a file called 
".license" in the freesurfer folder but am not sure why freesurfer is not 
recognising it. 

Many thanks in advance for your help!

sven



On 24-okt-2013, at 16:39, Z K wrote:

> Hi Sven,
> 
> Whats most likely happening is that you are defining SUBJECTS_DIR prior to 
> sourcing SetUpFreeSurfer.csh. Freesurfer will not overwrite the SUBJECTS_DIR 
> environment variable if it already exists at the time of sourcing the 
> SetUpFreeSurfer.csh. This is most likely occuring in your .cshrc file.
> 
> To verify, type 'echo $SUBJECTS_DIR' before sourcing and see what the output 
> says.
> 
> -Zeke
> 
> On 10/24/2013 09:10 AM, muellersvenc wrote:
>> Hi all,
>> 
>> I am running into trouble testing my freesurfer installation on a Mac 
>> (10.6.8). I followed all steps in the guide but there is something funny 
>> that freesurfer does not seem to recognise its own "subjects" directory (see 
>> attached screenshot). If screenshot is not visible, it says:
>> 
>>  freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 
>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>> WARNING: Applications/freesurfer/subjects does not exist
>> FREESURFER_HOME   /Applications/freesurfer
>> FSFAST_HOME   /Applications/freesurfer/fsfast
>> FSF_OUTPUT_FORMAT nii.gz
>> SUBJECTS_DIR  Applications/freesurfer/subjects
>> MNI_DIR   /Applications/freesurfer/mni
>> FSL_DIR   /usr/local/fsl
>> 
>> I think it might have to do with the fact that there is a "/" missing in 
>> front of the "Applications" but I don't know where/how to change this. I 
>> checked my StartUp.csh file and there everything seems fine. However, the 
>> subjects directory was definitely created by freesurfer (also screenshot) so 
>> there is a mismatch somewhere.
>> 
>> I am sure it is a simple thing but can someone please let me know what I 
>> should do so I can start to enjoy freesurfer?
>> 
>> Many thanks in advance,
>> 
>> sven
>> 
>> 
>> 
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> 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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Re: [Freesurfer] installation trouble - error message subjects directory not recognised

[Z K]

If there really is a .license in the FREESURFER_HOME directory then 
everything should be working fine. What is the output when you type:

'ls -l /Applications/freesurfer/.license'

at the command line? And what is the output when you type:

'ls -l $FREESURFER_HOME/.license'


On 10/24/2013 11:25 AM, muellersvenc wrote:
> Hi Zeke,
>
> that seems to have worked (strangely because I didn't really do anything 
> different before other than a fresh reinstall).
>
> However, now I have problems with the license file when trying to test the 
> installation as suggested on the "Testing your freesurfer installation" 
> webpage.
>
> I did a fresh installation, then created a ".license" file using the text 
> editor containing the three lines that were sent to me by email and placed 
> this file into the freesurfer folder which is my FREESURFER_HOME 
> (/Applications/freesurfer). Then I did the sourcing. And then when I type for 
> instance
>
> [pp05c332:/Applications] switch% tkmedit bert orig.mgz
> --
> ERROR: FreeSurfer license file /Applications/freesurfer/.license not found.
>If you are outside the NMR-Martinos Center,
>go to http://surfer.nmr.mgh.harvard.edu to
>get a valid license file (it's free).
>If you are inside the NMR-Martinos Center,
>make sure to source the standard environment.
> --
> [pp05c332:/Applications] switch%
>
>
> Any ideas what I am doing wrong? I changed the settings on my computer a 
> while ago and I can see the hidden files so can also see that there is a file 
> called ".license" in the freesurfer folder but am not sure why freesurfer is 
> not recognising it.
>
> Many thanks in advance for your help!
>
> sven
>
>
>
> On 24-okt-2013, at 16:39, Z K wrote:
>
>> Hi Sven,
>>
>> Whats most likely happening is that you are defining SUBJECTS_DIR prior to 
>> sourcing SetUpFreeSurfer.csh. Freesurfer will not overwrite the SUBJECTS_DIR 
>> environment variable if it already exists at the time of sourcing the 
>> SetUpFreeSurfer.csh. This is most likely occuring in your .cshrc file.
>>
>> To verify, type 'echo $SUBJECTS_DIR' before sourcing and see what the output 
>> says.
>>
>> -Zeke
>>
>> On 10/24/2013 09:10 AM, muellersvenc wrote:
>>> Hi all,
>>>
>>> I am running into trouble testing my freesurfer installation on a Mac 
>>> (10.6.8). I followed all steps in the guide but there is something funny 
>>> that freesurfer does not seem to recognise its own "subjects" directory 
>>> (see attached screenshot). If screenshot is not visible, it says:
>>>
>>>  freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 
>>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>>> WARNING: Applications/freesurfer/subjects does not exist
>>> FREESURFER_HOME   /Applications/freesurfer
>>> FSFAST_HOME   /Applications/freesurfer/fsfast
>>> FSF_OUTPUT_FORMAT nii.gz
>>> SUBJECTS_DIR  Applications/freesurfer/subjects
>>> MNI_DIR   /Applications/freesurfer/mni
>>> FSL_DIR   /usr/local/fsl
>>>
>>> I think it might have to do with the fact that there is a "/" missing in 
>>> front of the "Applications" but I don't know where/how to change this. I 
>>> checked my StartUp.csh file and there everything seems fine. However, the 
>>> subjects directory was definitely created by freesurfer (also screenshot) 
>>> so there is a mismatch somewhere.
>>>
>>> I am sure it is a simple thing but can someone please let me know what I 
>>> should do so I can start to enjoy freesurfer?
>>>
>>> Many thanks in advance,
>>>
>>> sven
>>>
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> 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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Re: [Freesurfer] [martinos-tech] FSFAST between-conditions contrasts

[Douglas N Greve]

Hi Sue, that looks correct. I think it is an open question as to whether 
you should use the corrected maps or use the uncorrected and then 
correct the final map. Maybe someone else can chime in.

doug


On 10/23/2013 09:49 AM, Susan Ruiz wrote:
> Hi Doug,
>
> This is /very/ helpful.
>
> Procedurally, would this be the correct approach?
>
> For positive % signal change from baseline clusters, use these files 
> resulting from mri_glmfit-sim:
> condAvFix.th3.pos.sig.cluster.nii
> condBvFix.th3.pos.sig.cluster.nii
> condAvscondB.th3.pos.sig.cluster.nii
>
> then run:
> % mri_concat --i condAvFix.th3.pos.sig.cluster.nii --i 
> condBvFix.th3.pos.sig.cluster.nii --i 
> condAvscondB.th3.pos.sig.cluster.nii --conjunct --o positive.AvsB.nii
>
> For negative % signal change from baseline clusters, use these files 
> resulting from mri_glmfit-sim:
> condAvFix.th3.neg.sig.cluster.nii
> condBvFix.th3.neg.sig.cluster.nii
> condAvscondB.th3.pos.sig.cluster.niigrf.th3.pos.sig.cluster.nii
>
> then run:
> % mri_concat --i condAvFix.th3.neg.sig.cluster.nii --i 
> condBvFix.th3.neg.sig.cluster.nii --i 
> condAvscondB.th3.pos.sig.cluster.nii --conjunct --o negative.AvsB.nii
>
> Note that for positive activation differences I would use sign=pos for 
> each condition vs fixation during mri_glmfit-sim, and for 
> "deactivation" clusters I use sign=neg for each condition vs fixation 
> during mri_glmfit-sim. BUT for both cases I use sign=pos for condition 
> A vs. condition B.
>
> Thanks so much!
>
> Best,
> ~Sue
>
>
>
> On Tue, Oct 22, 2013 at 10:50 AM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> Hi Sue, I agree that they are not the same thing. There is not a
> single
> flag that will do what you want. What you are describing is a post-hoc
> test. So you look for places where A != B, then within those
> voxels you
> do posthoc tests. You can implement this with a conjunction analysis
> where you set up threeway conjunction A>B and A>0 and B>0. You can do
> this with the --conjunt option to mri_concat
> doug
>
>
> On 10/21/2013 02:13 PM, Susan Ruiz wrote:
> > Hi all,
> >
> > When running a functional analysis and comparing two experimental
> > conditions, we observed that there are some voxels/vertices
> where both
> > condition A and condition B have a positive % signal change from
> > baseline, and condition A has greater activity than condition B.
> >
> > In other regions, both condition A and condition B have negative %
> > signal change from baseline, but condition B has a greater absolute
> > value % signal change (thus relative to baseline condition B has
> more
> > "deactivation"--a term I am using since you all know what I mean
> even
> > if the term itself is imperfect).
> >
> > Since, in both cases, the % signal change is technically
> condition A >
> > condition B, the between-conditions maps do not distinguish
> these two
> > scenarios. FS-FAST sees these as being the same. Is there a way to
> > tell FS-FAST to cluster these scenarios separately? Is there a
> > compelling reason why I should not consider these different
> > situations? It seems to me that the interpretation of what's taking
> > place in these two scenarios is not identical. Agree or
> disagree? Can
> > FS-FAST distinguish these with a flag I don't know about?
> >
> > Thank you,
> > ~Sue
> >
> > --
> > * * ** *** *  *
> > Susan Mosher Ruiz, Ph.D.
> > Research Scientist
> > Boston University School of Medicine
> > Laboratory of Neuropsychology
> > VA Boston Healthcare System
> > smos...@bu.edu   >
> > * * ** *** *  *
> >
>
> --
> 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/
>
>
>
> 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] Problem in final analysis

[Douglas N Greve]

Hi Carina, I still don't understand what you are trying to do. It looks 
like you have run the individual analysis (recon-all). Have you looked 
at the results for the individual? Do they look ok? QDEC is for group 
analysis, but you should make sure that the individuals look ok first
doug


On 10/23/2013 10:48 AM, car...@van-vlodrop.de wrote:
>
> Hi Doug,
>
>
> maybe I created the brain correctly with the file I mentioned.
>
> To try if there is the problem of a wrong brain or that there is a 
> problem just in uploading it in qdec I heard something about an 
> "example-brain" from freesurfer.
>
> Maybe it is possible to tell me where I can find this brain to use it 
> for my analysis in combination with my qdec table which I can upload 
> without problems.
>
>
> Carina
>
>
>
> - Ursprüngliche Nachricht -
>
>> Von: Douglas N Greve
>> Gesendet: 21.10.13 17:13 Uhr
>> An: freesurfer@nmr.mgh.harvard.edu
>> Betreff: Re: [Freesurfer] Problem in final analysis
>>
>>
>> fsaverage is already part of the distribution. I don't understand from
>> your email what the problem is.
>> doug
>>
>>
>>
>> On 10/21/2013 10:03 AM, car...@van-vlodrop.de wrote:
>> >
>> > Hi Doug,
>> >
>> >
>> > I have already run:
>> >
>> >
>> > recon-all -s subject -qcache -target avgsubject for each subject
>> >
>> >
>> > Is it the same file?
>> >
>> > I am not sure if the brain is really created or if there is a problem
>> > in uploading the brain in qdec.
>> >
>> > Is it possible to get the fsaverage brain from freesurfer to check the
>> > cause of the problem?
>> >
>> >
>> > Thank you
>> >
>> > Carina
>> >
>> >
>> >
>> >
>> >
>> >> - Ursprüngliche Nachricht -
>> >> Von: Douglas Greve
>> >> Gesendet: 28.09.13 17:46 Uhr
>> >> An: freesurfer@nmr.mgh.harvard.edu
>> >> Betreff: Re: [Freesurfer] Problem in final analysis
>> >>
>> >> Hi Carina, run
>> >>
>> >> recon-all -s subject -qcache
>> >>
>> >> for each subject and this will create the file
>> >>
>> >> doug
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> On 9/28/13 5:37 AM, car...@van-vlodrop.de wrote:
>> >>
>> >> Dear freesurfer community, we are conducting cortical-thickness
>> >> analysis using freesurfer-4.4.0 and have been experiencing some
>> >> problems with the final analysis steps. We are using the qdec.
>> >> Uploading of the data table has been successful. When we try to
>> >> use the “Analyze” command (design) in the qdec, we get the
>> >> following error message: Error in Analyze: Couldn’t open file
>> >> 
>> /data/projects/oertelmatura/Neurodegeneration/AJ83/surf/lh.thickness.fwhm10.fsaverage.mgh
>> >> Obviously, the file was never created during preprocessing. We
>> >> wonder, how to create dir/lh.thickness.fwhm10.fsaverage.mgh and
>> >> would be very grateful for your comments. Yours sincerely, Carina
>> >> $ bugr FREESURFER_HOME: /apps/prod/i486/freesurfer-4.4.0 Build
>> >> stamp: freesurfer-Linux-centos4-stable-pub-v4.4.0 Debian version:
>> >> 5.0.6 Kernel info: Linux 2.6.27.39- 1 –ql-beowulf i686 $ which
>> >> surfer -> /apps/prod/i486/freesurfer-4.4.0/bin/freesurfer Used
>> >> command: qdec/design/Analyze Error message: Error in Analyze:
>> >> Couldn’t open file
>> >> 
>> /data/projects/oertelmatura/Neurodegeneration/AJ83/surf/lh.thikness.fwhm10.fsaverage.mgh
>> >>
>> >>
>> >>
>> >> ___ Freesurfer
>> >> mailing list Freesurfer@nmr.mgh.harvard.edu
>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >>
>> >>
>> >
>> >
>> >
>> > ___
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>> >
>> >
>> > The information in this e-mail is intended only for the person to 
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>> the e-mail
>> > contains patient information, please contact the Partners 
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>> -- 
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>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
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Re: [Freesurfer] fast_selxavg3.m - ERROR: design is ill-conditioned

[Douglas N Greve]

Hi Ronny, you added 5 new conditions, so it should have increased by at 
least 5. However, if you are using a derivative with the HRF, then you 
will have 2 regressors for each condition and it will increase by 10.

I don't know why it does not like the 2nd one. Can you send me the 
Xtmp.mat file?

doug

On 10/23/2013 12:16 PM, preci...@nmr.mgh.harvard.edu wrote:
> I have two sets of identical blocks within each fMRI run, so conditions
> {1,2,3,4,5,1,2,3,4,5}, and there are three separate runs of the two blocks.
>
> If I run the analysis treating each with the contrasts set up with this
> numbering scheme (e.g. 3 vs 1 has two occurrences) , I get the following
> output from  /usr/local/freesurfer/dev/fsfast/toolbox/fast_selxavg3.m
>
> ...
> ntptot = 687, nX = 136, DOF = 551
> Saving X matrix to
> /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008/bold/improv.sm05.lh/Xtmp.mat
> XCond = 2926.01 (normalized)
>
> However, if I want to treat the two sets of blocks separately, i.e.,
> {1,2,3,4,5,6,7,8,9,10}
> so I can look at contrasts such as 3 vs 1 as well as 8 vs 6 then
> fast_selxavg3.m gives:
>
> ntptot = 687, nX = 146, DOF = 541
> Saving X matrix to
> /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block/bold/improv.10blocks.sm05.lh/Xtmp.mat
> XCond = 4.33238e+08 (normalized)
> ERROR: design is ill-conditioned
>
> 1) why does nX increase by 10 in the 2nd case?
> 2) why is fast_selxavg3.m unhappy and XCond so large? Can it not handle 10
> separate blocks?
>
> The entire log file in the 2nd case is attached.
>
>
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[Freesurfer] Extracting individuals data at a vertex

[O'Shea,Andrew]

Hello FS experts,
In QDEC when I click on a vertex a scatter plot is generated with each 
individuals data for that vertex. Is there a simple way to extract that data 
(for each subject) into spreadsheet form for a specific vertex?
-Andrew
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Re: [Freesurfer] mri_glmfit-sim with conjunction maps but without pre-cached data

[Douglas N Greve]

Hi Caspar, there are a couple of things you can do:

1. Go into the mri_glmfit folder used to create the input contrasts to 
the conjunction. Create a subfolder. Save the conjunction as sig.mgz and 
create a file called "C.dat" (it can be empty) in this folder. Then run 
mri_glmfit-sim specifying to do the simulation rather than using cached 
data.

2. Create cached data by running mri_mcsim. This may take longer than 
#1, but once you have the cached data you do not need to run it again, 
which could be useful if you are going to do more analyses with this 
template

doug


On 10/23/2013 02:55 PM, Caspar M. Schwiedrzik wrote:
> Hi,
> I have a question regarding cluster size thresholding using 
> mri_glmfit-sim. Namely, I have a sig.nii conjunction map that I made 
> with mri_concat.
> The analyses that serve as input to the conjunction map are done on a 
> custom surface template.
> If I want to run mri_glmfit-sim, how would that work? I obviously do 
> not have precached data.
> Thanks, Caspar
>
>
>
>
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[Freesurfer] label issues (converting from the MNI space to the Talairach space)

[Qi Wu]

Hi Freesurfer users,

I need to design a ROI map for my project. It has to be based on certain
coordinates. The ideal is to draw a circle based on the coordinates in the
Talairach space in Freesurfer, which I do not know how to achieve. The
alternative is to draw a spherical cluster in fsl and convert it back to
the Talairach space in Freesurfer, which I don't know how to do either.

Any suggestions?

Many thanks

Keith

Postdoc fellow
Toronto Western Hospital
Canada
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Re: [Freesurfer] Conversion niifty to dcm

[Douglas N Greve]

no we don't, sorry
On 10/24/2013 07:26 AM, std...@virgilio.it wrote:
> Hi list,
>
> there is a way to convert niifty or .par/.rec in DICOM?
>
> Thank you very much,
>
>
> Stefano
>
>
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Re: [Freesurfer] skull striping error question

[Douglas N Greve]

How far outside are they? Can you send a pic?
doug

On 10/23/2013 01:16 PM, Subhabrata Chaudhury wrote:
> Even the Supratentorial volume ? Supratentorial volume includes some 
> structures outside the surfaces ?
> Thanks
> Subha
>
>> - Original Message -
>>
>> From: Bruce Fischl
>>
>> Sent: 10/23/13 01:13 PM
>>
>> To: Subhabrata Chaudhury
>>
>> Subject: Re: [Freesurfer] skull striping error question
>>
>> You should be fine if the surfaces aren't affected by the remaining skull
>> Bruce
>> On
>> Wed, 23 Oct 2013, Subhabrata Chaudhury wrote:
>>
>> > Hi Everyone,
>> >
>> > I have some data where the skull striping hasnt worked properly and there 
>> > are some skull remaining.
>> > However, upon looking at the white and pial surfaces, those look perfectly 
>> > fine. My question is will the
>> > erroneous skullstriping affect the supratentorial volume estimation ?
>> > I will be highly obliged if someone can address this concern.
>> >
>> > Regards
>> >
>> > Subha
>> >
>> >
>>
>>
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>> addressed. If you believe this e-mail was sent to you in error and the e-mail
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>> properly
>> dispose of the e-mail.
>
>
>
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Re: [Freesurfer] Volumes in native or normalized space, and eTIV

[Douglas N Greve]

On 10/24/2013 10:37 AM, Dorian P. wrote:
> Dear all,
>
> Excuse if these are simple questions but I am a bit confused on the 
> significance of the volume measures.
>
> 1. Are the volumes of ROIs calculated after normalization?
No, everything is done in native space.
>
> 2. If volumes are calculated post-normalization, why is correction for 
> eTIV needed?
>
> 3. What is the quickest way to correct for eTIV?
Not sure what you mean by the "quickest". Usually the ROI volumes are 
divided by the eTIV or the eTIV is used as a regressor
doug
>
> Thank you.
> Dorian
> TJU
>
>
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Re: [Freesurfer] Extracting individuals data at a vertex

[Douglas N Greve]

You can do this, eg, to extract vertex 529

  mri_segstats --i /path/to/qdec/Untitled/y.mgh --seg 
$SUBJECTS_DIR/fsaverage/surf/lh.curv --sum junk.sum --id 1 --avgwf 
vertex.529.dat --vox 529 0 0

doug


On 10/24/2013 11:47 AM, O'Shea,Andrew wrote:
> Hello FS experts,
> In QDEC when I click on a vertex a scatter plot is generated with each 
> individuals data for that vertex. Is there a simple way to extract 
> that data (for each subject) into spreadsheet form for a specific vertex?
> -Andrew
>
>
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Re: [Freesurfer] fast_selxavg3.m - ERROR: design is ill-conditioned

[Douglas N Greve]

I think the problem is that the order of the conditions is always the 
same combined with an absence of fixation points. I don't think you can 
do this analysiswith this design.

doug


On 10/24/2013 12:08 PM, preci...@nmr.mgh.harvard.edu wrote:
> Xtmp.mat Attached
>
>
>> Hi Ronny, you added 5 new conditions, so it should have increased by at
>> least 5. However, if you are using a derivative with the HRF, then you
>> will have 2 regressors for each condition and it will increase by 10.
>>
>> I don't know why it does not like the 2nd one. Can you send me the
>> Xtmp.mat file?
>>
>> doug
>>
>> On 10/23/2013 12:16 PM, preci...@nmr.mgh.harvard.edu wrote:
>>> I have two sets of identical blocks within each fMRI run, so conditions
>>> {1,2,3,4,5,1,2,3,4,5}, and there are three separate runs of the two
>>> blocks.
>>>
>>> If I run the analysis treating each with the contrasts set up with this
>>> numbering scheme (e.g. 3 vs 1 has two occurrences) , I get the following
>>> output from  /usr/local/freesurfer/dev/fsfast/toolbox/fast_selxavg3.m
>>>
>>> ...
>>> ntptot = 687, nX = 136, DOF = 551
>>> Saving X matrix to
>>> /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008/bold/improv.sm05.lh/Xtmp.mat
>>> XCond = 2926.01 (normalized)
>>>
>>> However, if I want to treat the two sets of blocks separately, i.e.,
>>> {1,2,3,4,5,6,7,8,9,10}
>>> so I can look at contrasts such as 3 vs 1 as well as 8 vs 6 then
>>> fast_selxavg3.m gives:
>>>
>>> ntptot = 687, nX = 146, DOF = 541
>>> Saving X matrix to
>>> /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block/bold/improv.10blocks.sm05.lh/Xtmp.mat
>>> XCond = 4.33238e+08 (normalized)
>>> ERROR: design is ill-conditioned
>>>
>>> 1) why does nX increase by 10 in the 2nd case?
>>> 2) why is fast_selxavg3.m unhappy and XCond so large? Can it not handle
>>> 10
>>> separate blocks?
>>>
>>> The entire log file in the 2nd case is attached.
>>>
>>>
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>> --
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>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
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>>
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>>
> >

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Re: [Freesurfer] How do you create labels from binary masks?

[Douglas N Greve]

Can you load it properly in tksurfer?


On 10/23/2013 12:44 AM, Marcos Martins da Silva wrote:
>
> Hi, Doug
> Sorry for this late feedback.
> Just so you can understand what is binLeftHippoBody.mgz I will explain 
> its origin.
> 1) recon-all --hippo-subfields
> 2) mri_concat the posterior*.mgz to get the whole hippocampus
> 3) a custom octave routine to segment the whole hippocampus into head, 
> body and tail. This routine preserves the probability values of the 
> original posterior*.mgz
> 4) mri_binarize the whole hippocampus and its segments. So 
> binLeftHippoBody.mgz is the binary mask of left hippocampal body.
> 5) mri-tesselate and mris_smooth the whole hippocampus binary mask to 
> create a surface (lh.surfHippo)
>
> Now that is the reason I would like to get the surface labels for 
> head, body and tail. I would like to build a annot in order to display 
> the colored segments over the whole hippocampus surface.
> Your last tip was great and now I have vertex numbers at the labels 
> files  and mris_label2annot works. It follows the commands I used to 
> process the hippocampal body:
> mri_vol2surf --src binLeftHippoBody.mgz --out LeftHippoBody_surf.mgh 
> --out_type mgh --hemi lh --regheader suj1 --surf surfHippo
> mri_cor2label --i LeftHippoBody_surf.mgh --surf suj1 lh surfHippo --id 
> 1 --l lh.HippoBody.label
>
> I put the --surf parameter pointing to lh.surfHippo because, if not, 
> it would use lh.white (default). As I said it works but the results 
> are not visually correct (see attached file). The surface loads on 
> freeview with no problem but if I try to load the label representing 
> the body or the annot with the 3 segments they do not appear. It seems 
> only a small part of the vertices appears in blue. I also get the 
> following output at the terminal window I used to start freeview:
>
> MRISreadAnnotationIntoArray: vertex index out of range: 122882 
> i=, in_array_size=11627
> annot file: ../label/lh.Hippo.annot
> MRISreadAnnotationIntoArray: vertex index out of range: 122883 
> i=, in_array_size=11627
> annot file: ../label/lh.Hippo.annot
> MRISreadAnnotationIntoArray: vertex index out of range: 122884 
> i=, in_array_size=11627
> annot file: ../label/lh.Hippo.annot
> MRISreadAnnotationIntoArray: vertex index out of range: 122885 
> i=, in_array_size=11627
> annot file: ../label/lh.Hippo.annot
> reading colortable from annotation file...
> colortable with 4 entries read (originally ../label/Hippo.ctab)
> colortable with 4 entries read (originally ../label/Hippo.ctab)
> =, in_array_size=11627
>
> Since the posterior*.mgz files are 0.5 x 0.5 x 0.5 mm I also tried to 
> use mri_convert --vs 1 1 1, but it did not worked too.
> I guess, or at least, I hope I am closer the image I want but I guess 
> some more steps are necessary.
> Thank you for any help.
> Marcos
>
>
>
> Em Qui, 2013-10-17 às 22:19 -0400, Douglas Greve escreveu:
>>
>> Is *binLeftHippoBody.mgz a volume label or a surface label? If a 
>> volume label, map it onto the surface with mri_vol2surf, the run 
>> mri_cor2label *specifying --surf
>>
>> doug
>>
>>
>>
>>
>> On 10/17/13 5:00 PM, Marcos Martins da Silva wrote:
>>
>>> Hi, Doug
>>> Thank you for your answer.
>>>
>>> I am trying cor2label as you suggested. First of all I am afraid to 
>>> say that website documentation and help from the own command are a 
>>> bit different so I got a little confused. But the following command 
>>> worked: *mri_cor2label --i binLeftHippoBody.mgz --id 1 --l 2.leftBody*
>>>
>>> Using freeview I could load the hippocampus volume and 2.leftBody as 
>>> a ROI. I attached a screenshot that also included 1.leftHead and 
>>> 3.leftTail, generated in the same way.
>>> When I tried to concatenate the 3 labels into an annot file I got an 
>>> error:
>>>
>>> *mris_label2annot --s bert --h lh --ctab HippoColorLUT.txt --l 
>>> 1.leftHead.label --l 2.leftBody.label --l 3.leftTail.label --a 
>>> lefthippo*
>>> *Loading /home/marcos/freesurfer/subjects/bert/surf/lh.orig*
>>> *1 16711680 leftHead*
>>> *ERROR: 1.leftHead.label, n=0, vertex -1 out of range*
>>>
>>> When I checked label file generated by mri_cor2label the first 
>>> collumn (vertex number) contains only *-1* as value.
>>> It seems that when you use mri_cor2label it does not preserve or 
>>> even recover the vertex number. It also seems I need the correct 
>>> vertex number in label file to use mris_label2annot
>>> Just to rule out a problem with the hippocampal subfield files I 
>>> tried the example command (extracted from command help):
>>> mri_cor2label --i aseg.mgz --id 12 --l left-putamen.label
>>> This label also shows only -1 as vertex number.
>>>
>>> Could you please explain me what do I need to do to get the vertex 
>>> numbers in the label file as output of mri_cor2label?
>>>
>>> Cheers,
>>> Marcos
>>>
>>>
>>>
>>> Em Qua, 2013-10-16 às 20:34 -0400, Douglas Greve escreveu:
 I think you need to use mri_cor2label (not 

Re: [Freesurfer] Volumes in native or normalized space, and eTIV

[Dorian P.]

Thank you Douglas.

The eTIV has values like 1543825. Dividing ROIs by this value would create
very small values.

Is there a standard TIV (i.e. from the talairach brain) to use as
denominator for creating a ratio value? Or what is the best way to create a
reasonable factor (i.e. 0.7-1.3) to correct/normalize roi volumes?

Dorian



2013/10/24 Douglas N Greve 

>
> On 10/24/2013 10:37 AM, Dorian P. wrote:
> > Dear all,
> >
> > Excuse if these are simple questions but I am a bit confused on the
> > significance of the volume measures.
> >
> > 1. Are the volumes of ROIs calculated after normalization?
> No, everything is done in native space.
> >
> > 2. If volumes are calculated post-normalization, why is correction for
> > eTIV needed?
> >
> > 3. What is the quickest way to correct for eTIV?
> Not sure what you mean by the "quickest". Usually the ROI volumes are
> divided by the eTIV or the eTIV is used as a regressor
> doug
> >
> > Thank you.
> > Dorian
> > TJU
> >
> >
> > ___
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> > 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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>
>
> 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
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> but does not contain patient information, please contact the sender and
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> dispose of the e-mail.
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Re: [Freesurfer] Volumes in native or normalized space, and eTIV

[Bruce Fischl]

Why is a small # a problem? It simply represents the fraction of the 
total intracranial volume occupied by that structure.

cheers
Bruce
On Thu, 24 Oct 2013, 
Dorian P. wrote:

> Thank you Douglas.
> The eTIV has values like 1543825. Dividing ROIs by this value would create
> very small values.
> 
> Is there a standard TIV (i.e. from the talairach brain) to use as
> denominator for creating a ratio value? Or what is the best way to create a
> reasonable factor (i.e. 0.7-1.3) to correct/normalize roi volumes?
> 
> Dorian
> 
> 
> 
> 2013/10/24 Douglas N Greve 
>
>   On 10/24/2013 10:37 AM, Dorian P. wrote:
>   > Dear all,
>   >
>   > Excuse if these are simple questions but I am a bit confused
>   on the
>   > significance of the volume measures.
>   >
>   > 1. Are the volumes of ROIs calculated after normalization?
> No, everything is done in native space.
> >
> > 2. If volumes are calculated post-normalization, why is correction
> for
> > eTIV needed?
> >
> > 3. What is the quickest way to correct for eTIV?
> Not sure what you mean by the "quickest". Usually the ROI volumes are
> divided by the eTIV or the eTIV is used as a regressor
> doug
> >
> > Thank you.
> > Dorian
> > TJU
> >
> >
> > ___
> > 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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> Freesurfer@nmr.mgh.harvard.edu
> 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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[Freesurfer] v4.5.0: How to obtain total gray matter volume?

[Natalie Garcia]

Dear all,

I've been using Freesurfer v4.5.0 for some time and have reconned about 100
participants. I am wondering if there is an automatic way to obtain the
total gray matter volume for all the subjects I have run so far under this
version, or would it be necessary to update to v5.2?

Any help would be greatly appreciated!


Best,
Natalie
-- 
 Natalie V. Garcia
Graduate Student, Cognitive Psychology
Psychology Department
The Pennsylvania State University
423 Moore Building
nvg...@psu.edu
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[Freesurfer] Total WM volume

[Fotiadis, Panagiotis]

Hi FS Community,

Does the "Total cortical white matter volume" parameter in the aseg.stats file 
represent the total wm volume in the brain?

Thank you in advance,
Panos
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Re: [Freesurfer] installation trouble - error message subjects directory not recognised

[Z K]

Sven,

Well that certainly is odd that. My guess is that there is some sort of 
extension that Mac is hiding in the finder window (along the lines of 
what you were talking about with the text editor).

Im also a little concerned about the double '//' that is part of your 
FREESURFER_HOME environment variable. That should not be there, although 
I don't think its necessarily a problem.

Please open a terminal and type the following command:

'touch /Applications/freesurfer/.license'

That should fix your problem. Let me know if not. Also, please CC the 
list on these responses so that they can be stored for others to view.

-Zeke


On 10/24/2013 02:29 PM, muellersvenc wrote:
> Hi Zeke,
>
> the output in both cases is: "no such file or directory".  I have attached a 
> screenshot to this email and you can see my freesurfer directory and the 
> .license file at the very top. Is this maybe a problem with creating such a 
> file with the text editor? There is also a file called LICENSE in the 
> directory but this just contains the license agreement.
>
> I really appreciate you helping me as I am keen on getting freesurfer to 
> work. So, thank you so much for your time and effort in helping me through 
> this! Much appreciated!
>
> Sven
>
>
>
>
>
> On 24-okt-2013, at 17:35, Z K wrote:
>
>> If there really is a .license in the FREESURFER_HOME directory then 
>> everything should be working fine. What is the output when you type:
>>
>> 'ls -l /Applications/freesurfer/.license'
>>
>> at the command line? And what is the output when you type:
>>
>> 'ls -l $FREESURFER_HOME/.license'
>>
>>
>> On 10/24/2013 11:25 AM, muellersvenc wrote:
>>> Hi Zeke,
>>>
>>> that seems to have worked (strangely because I didn't really do anything 
>>> different before other than a fresh reinstall).
>>>
>>> However, now I have problems with the license file when trying to test the 
>>> installation as suggested on the "Testing your freesurfer installation" 
>>> webpage.
>>>
>>> I did a fresh installation, then created a ".license" file using the text 
>>> editor containing the three lines that were sent to me by email and placed 
>>> this file into the freesurfer folder which is my FREESURFER_HOME 
>>> (/Applications/freesurfer). Then I did the sourcing. And then when I type 
>>> for instance
>>>
>>> [pp05c332:/Applications] switch% tkmedit bert orig.mgz
>>> --
>>> ERROR: FreeSurfer license file /Applications/freesurfer/.license not found.
>>>If you are outside the NMR-Martinos Center,
>>>go to http://surfer.nmr.mgh.harvard.edu to
>>>get a valid license file (it's free).
>>>If you are inside the NMR-Martinos Center,
>>>make sure to source the standard environment.
>>> --
>>> [pp05c332:/Applications] switch%
>>>
>>>
>>> Any ideas what I am doing wrong? I changed the settings on my computer a 
>>> while ago and I can see the hidden files so can also see that there is a 
>>> file called ".license" in the freesurfer folder but am not sure why 
>>> freesurfer is not recognising it.
>>>
>>> Many thanks in advance for your help!
>>>
>>> sven
>>>
>>>
>>>
>>> On 24-okt-2013, at 16:39, Z K wrote:
>>>
 Hi Sven,

 Whats most likely happening is that you are defining SUBJECTS_DIR prior to 
 sourcing SetUpFreeSurfer.csh. Freesurfer will not overwrite the 
 SUBJECTS_DIR environment variable if it already exists at the time of 
 sourcing the SetUpFreeSurfer.csh. This is most likely occuring in your 
 .cshrc file.

 To verify, type 'echo $SUBJECTS_DIR' before sourcing and see what the 
 output says.

 -Zeke

 On 10/24/2013 09:10 AM, muellersvenc wrote:
> Hi all,
>
> I am running into trouble testing my freesurfer installation on a Mac 
> (10.6.8). I followed all steps in the guide but there is something funny 
> that freesurfer does not seem to recognise its own "subjects" directory 
> (see attached screenshot). If screenshot is not visible, it says:
>
>  freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> WARNING: Applications/freesurfer/subjects does not exist
> FREESURFER_HOME   /Applications/freesurfer
> FSFAST_HOME   /Applications/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  Applications/freesurfer/subjects
> MNI_DIR   /Applications/freesurfer/mni
> FSL_DIR   /usr/local/fsl
>
> I think it might have to do with the fact that there is a "/" missing in 
> front of the "Applications" but I don't know where/how to change this. I 
> checked my StartUp.csh file and there everything seems fine. However, the 
> subjects directory was definitely created by freesurfer (also screenshot) 
> so there is a mismatch somewhere.
>
> I am sure

Re: [Freesurfer] problem with freesurfer installation/tkmedit

[Louis Nicholas Vinke]

Hi Elissa,
The invalid drawable terminal output you can ignore when running Freeview.

Presumably bert is not located in /Applications/freesurfer/elissa_thesis/, 
so that's why the bert commands are failing.  Not the same subjects 
directory that ABU is in.


To fix the tkmedit library error it looks like you just need to install 
xquartz on your mac.


http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg26311.html

The recon-all.log for the 8.5hr recon looks fine.  Was it processed 
locally and does your mac have a solid-state drive by chance?


-Louis

On Tue, 22 Oct 2013, Elissa McIntosh wrote:



Hi, I think there is a problem with my freesurfer installation (newest version 
5.3). First, when
trying this freeview command (see below) I found on the “Testing your 
freesurfer installation” page
using my own data, freesurfer opened, but I am concerned about the “invalid 
drawable” lines. The
message happened when I ran this command on the "bert" data.

 

[CoS-Psychology-Murphy-iMac-QAD:/Applications/freesurfer] cmurphy% freeview -v
$SUBJECTS_DIR/ABU/mri/norm.mgz -v 
$SUBJECTS_DIR/ABU/mri/aseg.mgz:colormap=lut:opacity=0.2 -f
$SUBJECTS_DIR/ABU/surf/lh.white:edgecolor=yellow -f 
$SUBJECTS_DIR/ABU/surf/rh.white:edgecolor=yellow
-f $SUBJECTS_DIR/ABU/surf/lh.pial:annot=aparc:edgecolor=red -f
$SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red

2013-10-22 12:47:02.811 Freeview[4214:703] invalid drawable

2013-10-22 12:47:02.812 Freeview[4214:703] invalid drawable

2013-10-22 12:47:02.826 Freeview[4214:703] invalid drawable

2013-10-22 12:47:02.826 Freeview[4214:703] invalid drawable

2013-10-22 12:47:02.839 Freeview[4214:703] invalid drawable

2013-10-22 12:47:02.840 Freeview[4214:703] invalid drawable

2013-10-22 12:47:02.853 Freeview[4214:703] invalid drawable

2013-10-22 12:47:02.853 Freeview[4214:703] invalid drawable

reading colortable from annotation file...

colortable with 36 entries read (originally
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)

colortable with 36 entries read (originally
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)

MRISread(/Applications/freesurfer/elissa_thesis/bert/surf/rh.pial): could not 
open file

No such file or directory

MRISread failed

MRISread(/Applications/freesurfer/elissa_thesis/bert/surf/rh.pial): could not 
open file

rfer/average/colortable_desikan_killiany.txt)

reading colortable from annotation file...

colortable with 36 entries read (originally
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)

colortable with 36 entries read (originally
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)

CTABisEntryValid: index -1 was OOB

No such file or directory

CTABisEntryValid: index -1 was OOB

No such file or directory

CTABisEntryValid: index -1 was OOB

iginally 
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)

CTABisEntryValid: index -1 was OOB

No such file or directory

CTABisEntryValid: index -1 was OOB

No such file or directory

CTABisEntryValid: index -1 was OOB

No such file or directory

CTABisEntryValid: index -1 was OOB

No such file or directory

CTABisEntryValid: index -1 was OOB

iginally 
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)

 

 

Second, my next issue is that I am unable to use tkmedit to view my data. See 
command below and
error message.

 

[CoS-Psychology-Murphy-iMac-QAD:/Applications/freesurfer] cmurphy% tkmedit ABU 
orig.mgz

dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib

  Referenced from: /Applications/freesurfer/tktools/tkmedit.bin

  Reason: image not found

Trace/BPT trap



I've tried other tkmedit commands and have gotten same error messages. I tried commands 
on "bert"
data but got same errors.

Third, I'd like to know if it is normal that a recon all could only take 
between 8-9 hours.

I have attached the recon-all.log for the subject I am trying to view. Here is 
some additional
information about my mac incase you see any glaring system inadequacies.

Processor  2.5 GHz Intel Core i5
Memory  4 GB 1333 MHz DDR3
Graphics  AMD Radeon HD 6750M 512 MB
Software  Mac OS X Lion 10.7.5 (11G63)


Thank you,
Elissa

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[Freesurfer] longitudinal measures

[Qi Wu]

Hi Freesurfer users,

For the longitudinal stream in FS5.1, there are only 4 options of measures
(do-avg, do-rate, do-pc1 and do-spc). However, if I need other measures,
such as the difference between two time points (thick2-thick1), how should
I do to get the values and still be able to do the voxel-wise analysis for
regional difference in cortical thickness (with glmfit)?

Many thanks

Keith
Postdoc research fellow
Toronto Western Hospital


   1.

   The temporal average is simply the average thickness: *avg = 0.5 *
   (thick1 + thick2)*
   2.

   The rate of change is the difference per time unit, so *rate = ( thick2
   - thick1 ) / (time2 - time1)*.
   3.

   The percent change (pc1) is the rate with respect to the thickness at
   the first time point: *pc1 = rate / thick1*.
   4.

   The symmetrized percent change (spc) is the rate with respect to the
   average thickness: *spc = rate / avg*.
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[Freesurfer] Incorrect orientations from MRI convert

[Chiu, Bryan (PHTH)]

Hi,

I am working on a dataset using free surfer.

I have NIFTII files which I am converting using mri_convert. Upon completion of 
mri_convert, the orientations of the files are wrong. This likely leads to an 
incorrect talairach (I was getting errors but used -notal-check) and leads to 
an incorrect labelling of volumes from the -autorecon-all.

My sagittal view is rotated 90 degrees clockwise on the MRI convert. The 
sagittal and coronal views are swapped. This appears in a tkmedit of the 
converted file.

error codes during mri_convert are as follows:

$ mri_convert 
'/Applications/freesurfer/subjects/001test/x-file-xx.nii.gz' 
'/Applications/freesurfer/subjects/001test/''orig2.mgz'
mri_convert 
/Applications/freesurfer/subjects/001test/x-file-xx.nii.gz.nii.gz 
/Applications/freesurfer/subjects/001test/orig2.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from 
/Applications/freesurfer/subjects/001test/HANDY_POWER_001_10_1_NIFTI.nii.gz...
WARNING: neither NIfTI-1 qform or sform are valid
WARNING: your volume will probably be incorrectly oriented
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
WARNING: it does not appear that there was sufficient information
in the input to assign orientation to the volume...
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to /Applications/freesurfer/subjects/001test/orig2.mgz

guidance to fix this would be appreciated.

- Bryan
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Re: [Freesurfer] Incorrect orientations from MRI convert

[Douglas N Greve]

How do you know the nifti files are correctly oriented to begin with?
doug
On 10/24/2013 07:07 PM, Chiu, Bryan (PHTH) wrote:
> Hi,
>
> I am working on a dataset using free surfer.
>
> I have NIFTII files which I am converting using mri_convert. Upon 
> completion of mri_convert, the orientations of the files are wrong. 
> This likely leads to an incorrect talairach (I was getting errors but 
> used -notal-check) and leads to an incorrect labelling of volumes from 
> the -autorecon-all.
>
> My sagittal view is rotated 90 degrees clockwise on the MRI convert. 
> The sagittal and coronal views are swapped. This appears in a tkmedit 
> of the converted file.
>
> error codes during mri_convert are as follows:
>
> $ mri_convert 
> '/Applications/freesurfer/subjects/001test/x-file-xx.nii.gz' 
> '/Applications/freesurfer/subjects/001test/''orig2.mgz'
> mri_convert 
> /Applications/freesurfer/subjects/001test/x-file-xx.nii.gz.nii.gz 
> /Applications/freesurfer/subjects/001test/orig2.mgz
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from 
> /Applications/freesurfer/subjects/001test/HANDY_POWER_001_10_1_NIFTI.nii.gz...
> WARNING: neither NIfTI-1 qform or sform are valid
> WARNING: your volume will probably be incorrectly oriented
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> WARNING: it does not appear that there was sufficient information
> in the input to assign orientation to the volume...
> i_ras = (-1, 0, 0)
> j_ras = (0, 1, 0)
> k_ras = (0, 0, 1)
> writing to /Applications/freesurfer/subjects/001test/orig2.mgz
>
> guidance to fix this would be appreciated.
>
> - Bryan
>
>
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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
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] How do you create labels from binary masks?

[Douglas N Greve]

areyou loading the label (output of mri_cor2label) or did you create an 
annotation? Try loading the label. Then try loading 
LeftHippoBody_surf.mgh. If that does not look ok, check the registration 
between binLeftHippoBody.mgz and subj1 with --regheader

doug

On 10/24/2013 06:40 PM, Marcos Martins da Silva wrote:
> Hi, Doug
> Thanks again for your help.
> Using the command tksurfer suj1 lh surfHippo, I get the surface loaded 
> in tksurfer in the same way that I get in freeview. The only 
> difference is that the terminal window output is more verbose and that 
> is valuable when investigating this kind of situation. I am attaching 
> a screenshot. I got this just after I used tksurfer to import an 
> annotation (lh.surfHippo + hippo.annot.png).
> The screenshot show just a few vertices with color. Indeed this is 
> similar to what we see in freeview, except that in this last tool all 
> vertices not in label appears in black and tksurfer preserves the gray 
> color.
> At terminal output  we can see tksurfer expects the surface refers to 
> lh.white. That is not the case, I guess. I think it helps explain the 
> terminal window output we see in freeview and also in tksurfer when I 
> try to load the annot file. It seems we have lots of vertices in annot 
> file that both tools cannot find in surface file and at the same time 
> we have lots of vertices in my surface file not described in the annot 
> files. At least now I can understand the situation. It puzzles me 
> because the surface, binary masks, labels and annotations were created 
> from the same source: the posterior*.mgz files created by recon-all 
> --hippo-subfields. But, well, I probably misunderstood something in 
> documentation and lost my way in some point. I hope you can help me 
> with the correct steps to be followed. I still dream of showing the 
> hippocampus in a similar way we do with cortex when we load lh.pial 
> and lh.aparc.annot.
> Thank you for your help and attention.
> Cheers,
> Marcos.
> Em Qui, 2013-10-24 às 12:40 -0400, Douglas N Greve escreveu:
>> Can you load it properly in tksurfer?
>>
>>
>> On 10/23/2013 12:44 AM, Marcos Martins da Silva wrote:
>> >
>> > Hi, Doug
>> > Sorry for this late feedback.
>> > Just so you can understand what is binLeftHippoBody.mgz I will explain
>> > its origin.
>> > 1) recon-all --hippo-subfields
>> > 2) mri_concat the posterior*.mgz to get the whole hippocampus
>> > 3) a custom octave routine to segment the whole hippocampus into head,
>> > body and tail. This routine preserves the probability values of the
>> > original posterior*.mgz
>> > 4) mri_binarize the whole hippocampus and its segments. So
>> > binLeftHippoBody.mgz is the binary mask of left hippocampal body.
>> > 5) mri-tesselate and mris_smooth the whole hippocampus binary mask to
>> > create a surface (lh.surfHippo)
>> >
>> > Now that is the reason I would like to get the surface labels for
>> > head, body and tail. I would like to build a annot in order to display
>> > the colored segments over the whole hippocampus surface.
>> > Your last tip was great and now I have vertex numbers at the labels
>> > files  and mris_label2annot works. It follows the commands I used to
>> > process the hippocampal body:
>> > mri_vol2surf --src binLeftHippoBody.mgz --out LeftHippoBody_surf.mgh
>> > --out_type mgh --hemi lh --regheader suj1 --surf surfHippo
>> > mri_cor2label --i LeftHippoBody_surf.mgh --surf suj1 lh surfHippo --id
>> > 1 --l lh.HippoBody.label
>> >
>> > I put the --surf parameter pointing to lh.surfHippo because, if not,
>> > it would use lh.white (default). As I said it works but the results
>> > are not visually correct (see attached file). The surface loads on
>> > freeview with no problem but if I try to load the label representing
>> > the body or the annot with the 3 segments they do not appear. It seems
>> > only a small part of the vertices appears in blue. I also get the
>> > following output at the terminal window I used to start freeview:
>> >
>> > MRISreadAnnotationIntoArray: vertex index out of range: 122882
>> > i=, in_array_size=11627
>> > annot file: ../label/lh.Hippo.annot
>> > MRISreadAnnotationIntoArray: vertex index out of range: 122883
>> > i=, in_array_size=11627
>> > annot file: ../label/lh.Hippo.annot
>> > MRISreadAnnotationIntoArray: vertex index out of range: 122884
>> > i=, in_array_size=11627
>> > annot file: ../label/lh.Hippo.annot
>> > MRISreadAnnotationIntoArray: vertex index out of range: 122885
>> > i=, in_array_size=11627
>> > annot file: ../label/lh.Hippo.annot
>> > reading colortable from annotation file...
>> > colortable with 4 entries read (originally ../label/Hippo.ctab)
>> > colortable with 4 entries read (originally ../label/Hippo.ctab)
>> > =, in_array_size=11627
>> >
>> > Since the posterior*.mgz files are 0.5 x 0.5 x 0.5 mm I also tried to
>> > use mri_convert --vs 1 1 1, but it did not worked too.
>> > I guess, or at least,