Hi Jeff,
you can run recon-all with flags -autorecon1, -gcareg, -canorm, -careg,
-careginv, -rmneck, -skull-lta and -calabel if
you want to generate files upto aseg.mgz. Please refer to this wiki for more
details about the flags.
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.
You might want to create a template from these datasets for any group
analysis you might be doing but just for running recon-all, you don't need
to.
It's not necessary to separate them in age ranges to create an average.
Sita.
On Fri, 5 Aug 2011, Felipe Picon wrote:
> Dear FreeSurfer experts
Hi Christopher,
If you want to upload the dataset, I can take a look.
Sita.
On Fri, 9 Sep 2011, Christopher Luna wrote:
> Hello,
>
> After running an *.img file through autorecon1. Freesurfer says it finishes
> with errors, but I cannot find any error messages in the command line
> output. Ch
Hi Mike,
I think you can run mri_surf2surf with --sval-annot flag. Try
mri_surf2surf --help for more options.
Sita.
On Mon, 12 Sep 2011, mbric...@nmr.mgh.harvard.edu wrote:
> Hi FS team,
> Is it possible to project an entire annotation file from one subject's
> surface to another? I haven't
How does the wm.mgz look. Correcting the white surface will correct the
pial surface as well.
Sita.
On Thu, 15 Sep 2011, Jing Ming wrote:
>
> Hi Surfers:
>We have been coming
> across several gray matter regions that are not included within the pial
> surface (red line) when it should be
Hi Pernille,
The shift doesn't really effect any edits or processing you might be doing
on the datasets. But if you want to get rid of it, on the tkmedit tools
window, you can select View -> Anatomical Resampling -> Main Volume/Aux
volume -> Slice.
Sita.
On Fri, 21 Oct 2011, Bruce Fischl wr
Hi Mahinda,
I can take a look if you want to upload a dataset. Please find
the instructions to upload in this wiki.
http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
Thanks,
Sita.
On Sat, 25 Feb 2012, Mahinda Yogarajah wrote:
Dear Freesurfer Experts,
Would it be easier to upload
Hi Julia,
Please try deleting the space in 'Left Amygdala' and 'Right Amygdala' in
your test.dat file and rerun qdec.
Sita.
On Wed, 7 Mar 2012, Richter, Julia wrote:
> Dear Sir or Madam,
>
> I have a question concerning FreeSurfer. At the moment I am trying to run a
> qdec analysis. I have
Hi Tanja,
Sorry if I missed something but was the cortex stripped off even
before you made any edits. If so, it's probably skull strip error. Please
refer to this wiki for instructions to correct the error.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix
But if part of the
Hi Charlotte,
If the skull/neck that's left off is not affecting the surfaces, it should
be okay. Skull strip looks okay too but it's hard to tell from one slice.
Sita.
On Tue, 17 Apr 2012, Charlotte Bernard wrote:
>
> From: chak...@live.fr
> To: freesurfer@nmr.mgh.harvard.edu
> Subject:
> D
Hi Anne,
What's the error message when you are running waterthreshold 25
Sita
On Wed, 23 May 2012, Anne Uhlmann wrote:
> Hi Freesurfers,
>
> I have problems with the troubleshoot of a scan that didn't run at all
> within autorecon (while the scan actually looks good).
> So I ran the skullstri
You can try
unsetenv SUBJECTS_DIR /tmp/qdec_project_archive
and set the SUBJECTS_DIR to the right directory again.
Sita.
On Tue, 3 Feb 2009, Lucia Garrido wrote:
Many thanks for your e-mail.
Yes, I've noticed that. But I made sure the SUBJECTS_DIR is the right one.
Everything else is run
Hi,
Looking at the data you have sent us, the surfaces look okay. No edits
are needed.
That bubble in the ventricle in Coronal view is labeled as Choroid
plexus. Future freesurfer versions will fill the choroid as well.
Sita.
On Mon, 9 Feb 2009, karlkarl wrote:
Hello, I sending in tw
Make sure you are selecting the 'Edit segmentation tool' on the tkmedit
tools window. You can also press the 'g' key to select the tool.
Sita.
On Thu, 19 Feb 2009, Silvia biopanda wrote:
Hi,
we are making changes in the aseg.mgz and we need to know how to erase
a wrong pixels. we read in
Hi Nasim,
1-Will I get accurate results if I do the edits (erasing misclassified
white
matter in wm.mgz) to my white matter mask only in those 10% areas that
the wm
surface is not accurate or should I correct the wm.mgz 'every where' no
matter what?
You can just make edits in the problem
Hi Gabriel,
In the snapshots you've sent, it doesn't look like there is an option
selected in the 'custom fill --> fill conditions'
You have to select 'custom fill --> fill conditions --> Upto and including
paths' along with the 'last clicked vertex' and 'create new label'.
Also make sure to c
Hi Kelly,
I think you can use mri_label2vol.
Try 'mri_label2vol --help' for more options.
Sita.
On Mon, 27 Apr 2009, Kelly Silva wrote:
Hello,
How can I convert one file *.label into *.img?
Thanks in advance.
Best regards, Kelly
Veja quais sã
Hi Ed,
You can try inserting a backslash and then a space in the filename.
eg.. if you have 'dicom file.dcm', you might want
to try
recon-all -all -i dicom\ file.dcm -s .
Sita.
On Wed, 6 May 2009, Ed Gronenschild wrote:
Hi,
Whenever I want to convert DICOM files to .mgz f
Hi Athena,
Small pieces of skull left is fine as long as the surfaces look okay.
But if they don't or if you want to edit the skull for any other reason,
you can do it manually but be careful not to edit the grey matter, which will
affect the surfaces.
If there is a large chunk of skull remain
Hi Jesse,
The DTI images are not stored in a way such that unpacksdcmdir can do a
proper error check and so it displays an error.
I think you can ignore the error.
Sita.
On Thu, 21 May 2009, Jesse Friedman wrote:
I've noticed that an error is consistently reported in the unpack log fil
Hi Karl,
After the white matter edits, you can run
recon-all -autorecon2-wm -autorecon3 -s
The old files will be overwritten.
Please refer to this wiki for more information on recon-all
http://surfer.nmr.mgh.harvard.edu/fswiki/recon-all
Sita.
On Thu, 11 Jun 2009, karlkarl wrote:
Hel
're-run with force' means that the subject name exists and using the
'force' flag will overwrite it.
As for the error, the info in this post might be helpful.
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06793.html
On Thu, 18 Jun 2009, Ahmed, F, Me wrote:
Hello,
What d
It's because "Brain Segmentation Volume Without Ventricles" stat is
computed with partial volume correction but "Number of Brain Segmentation Voxels" stat
is not. Please refer to this wiki for more info.
https://surfer.nmr.mgh.harvard.edu/fswiki/BrainVolume
Sita
On Wed, 1 Jul 2009, Jared
After fixing the Talairach registration, you need to rerun the whole
recon-all process. The old files will be overwritten.
recon-all -all -s
And after adding control points, you need to run,
recon-all -autorecon2-cp -autorecon3 -s
Sita.
On Thu, 16 Jul 2009, Ritobrato Datta wrote:
Hel
Hi Sameer,
I don't think it'll affect your results, but before you rerun recon-all
with -notal-check flag, check the registration in tkregister2 and make
sure it's correct.
Sita.
On Wed, 22 Jul 2009, sameer kumar wrote:
> hi all,
> I ran recon-all on a case, and it exited with errors, and
Hi Liz,
I think you can run tkregister2 with --noedit flag to convert .lta
files to .dat files.
tkregister2 --mov <..> --s <..> --lta <...> --noedit --reg
Sita.
On Tue, 4 Aug 2009, Elizabeth Selgrade wrote:
> Martin and FreeSurfer Users,
>
> A few more questions. What is the best way to
Hi Dana,
Does the talairach registration look okay.
And how do orig.mgz/nu.mgz look.
Sita.
On Wed, 5 Aug 2009, Dana W. Moore wrote:
> Hi,
>
> I have tried to run recon-all on an image and received the following error:
>
> "White matter intensity 0 is lower than CSF intensity 19. Please
> exa
I think the brainmask looks fine.
In general, tissue being stripped off or large chunks of skull left
behind should be corrected as explained in the wiki.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix
But small pieces of skull left is okay as long as
it's not affecting
Hi Zeng,
Here's the wiki for mris_volmask.
https://surfer.nmr.mgh.harvard.edu/fswiki/mris%25volmask
You can also find a description of it in the terminal window when you type
in 'mris_volmask --help' or just mris_volmask.
Sita.
On Thu, 10 Sep 2009, Guang Zeng wrote:
>
> Hello, there,
>
>
Hi Sherri,
Control points are meant to normalize the intensity of white matter
voxels to 110 and will not help if you are adding them in an
area of wm.mgz where the intensity is already 110.
If it's not working, you might want to make some edits in the
wm.mgz i.e. adding/deleting white matter
If no edits are made in the volume loaded as your main volume in tkmedit,
then the 'Save Main Volume' options appear in gray.
Sita.
On Wed, 4 Nov 2009, Gonzalo Rojas wrote:
> Hi:
>
> Why the options "Save Manin Volume" and "Save Main Volume as" in
> TkMedit' "File" menu appears in gray (d
You can run recon-all with -nonormalization flag, which will skip that
step.
Sita.
On Thu, 12 Nov 2009, africa millan wrote:
>
> Hello,
>
>
>
> Another question:If during the first recon-all, freesurfer makes
> skullstripping and normalization automatically... Is there any way to run the
Hi Africa,
-nonormalization flag skips the step where T1.mgz is generated which is
causing the error, as you mentioned. 001.mgz initiates the recon-all, but
there are several other steps and files generated in the process.
Please refer to this wiki to see which steps and the output at each st
Hi Meghana,
Depending on whether wm.mgz (or the volume in which you wish to make the edits)
is loaded as the main volume or aux
volume, you should select the target in the 'Tools' --> 'Configure Brush Info'
as either main or aux respectively.
In the example you are referring to, wm2_edits_bef
Hi Johanna,
This is probably a topological defect. Please follow
the steps in this wiki to correct the surfaces.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect
Sita.
On Thu, 11 Feb 2010, johanna feiler wrote:
Dear freesurfer experts,
After running the autorecon2
Hi Lena,
bbregister tool performs within-subject, cross-modal registration. I
think poor registration is probably because you are using fsaverage.
Sita.
On Fri, 12 Feb 2010, Lena Palaniyappan wrote:
>
>
>
> On 12/02/2010 16:47, "Lena Palaniyappan"
> wrote:
>
>> I want to use contrast files
Hi Jan,
Please try rerunning recon-all after removing the spaces or special
characters (if there are any) in the dicom files.
Sita.
On Mon, 22 Feb 2010, Janani Dhinakaran wrote:
> Is this what you meant:
>
> First I tried
> s0964...@cric-0012:~$ recon-all
> home/s0964091/Desktop/Allimages/M
es/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001/mri/orig/002.mgz...
>
> #--
>
> recon-all finished without error at Mon Feb 22 16:08:03 GMT 2010
> done
>
> It didn't recon ALL.
>
> Anyone know what I'm doing wrong?
&
Hi Corinna,
What is the command line that you are trying.
On Tue, 9 Mar 2010, corinna bauer wrote:
> Hello,
> I am running bbregister with pet scans and a number of the subject's
> registrations were poor. What is the best way to fix inaccurate
> coregistrations from bbregister?
>
> Regards,
Hi Mike,
Did you check the talairach. And how do nu.mgz and T1.mgz look.
Also you could probably try running the following command to see if the
skull strip step finishes without errors.
recon-all -skullstrip -no-wsgcaatlas -s
Sita.
On Thu, 18 Mar 2010, Michael Waskom wrote:
> Hi Bruce, N
rm
> and it looks generally alright, although I think it could be improved with
> some tweaking. It passed the automatic failure detection each time I ran
> recon-all, though. Would you recommend trying to improve the transform so
> that things down the line run more smoothly?
>
> Best,
Hi Hannah,
mris_anatomical_stats computes anatomical properties. To map the label, I
think you can use mri_label2label.
Sita.
On Fri, 19 Mar 2010, Bruehl, Hannah wrote:
>
> Hi there,
>
> I have got 2 questions:
>
> 1) is there way to use mris_anatomical_stats to map back the label I have
>
aching the recon-all.log file. Do
> you have any idea what might be causing this problem?
>
> Thanks,
> Mike
>
> On Thu, Mar 18, 2010 at 2:54 PM, Sita Kakunoori
> wrote:
>
>>
>> Hi Mike,
>>
>> I don't think the motion artifact could've been
There should be a -s before the subjectID. So the command line is
recon-all -make all -s
Thanks,
Sita.
On Wed, 24 Mar 2010, Sita Kakunoori wrote:
>
> Hi Mike,
>
> It seems that it usually happens when the surfaces have been rebuilt and
> the aparc is out of date (and need
Please refer to this wiki for definitions.
https://surfer.nmr.mgh.harvard.edu/fswiki/BrainVolume
On Thu, 25 Mar 2010, Gonzalo Rojas Costa wrote:
Hi:
What is the definition of the following measures that appears at the
beginning of "aseg.stats" file: "Brain Mask Volume", "Brain Segmentatio
Hi Sherri,
one of the control points seems to be in gray matter, which is probably
causing this. Please try deleting it and rerunning autorecon2-cp.
Sita.
On Tue, 6 Apr 2010, Sherri Novis wrote:
> Hello brilliant and generous FS people,
>
> I have introduced a problem I cannot solve. I am
Hi Christopher,
the values in wmparc.stats are computed with partial volume correction.
Sita.
On Wed, 12 May 2010, Christopher Coello wrote:
Hello,
After segmenting using recon-all all, I want to look at how much voxels
there is in each segmented structure.
I did the following procedur
For upsampling you can try the command,
mri_convert -vs 0.1 0.1 0.1
On Mon, 24 May 2010, EDSB EDSB wrote:
Hi all,
I have a question on the mri_convert command.
I should
up-sample my dataset (a list of COR files contained in the folder T1)
that has a matrix of 256 x 256 x 256 and a voxel
Hi Natalie,
I am not sure why, because this command is working for me.
Which version of freesurfer are you using. Also I am not sure if it helps,
but instead of overwriting the input file, can you try a different name
for the output and see if that works.
Sita.
On Fri, 4 Jun 2010, casp...@c
Hi Natalie,
Please ignore my previous e-mail. Doug suggested this work-around. You
can use the output from your mri_convert for the --targ flag in the following
command.
mri_vol2vol --mov original.nii --targ mriconvertoutput.nii --regheader --o
orig.new.nii
Thanks,
Sita.
> On Fri, 4 Jun 2
Hi Dave,
001.mgz in /mri/orig/ looks okay but 002.mgz looks strange,
which I think is the reason for what you are seeing in T1.mgz.
Did you collect 2 runs for structurals. Can you point me to the dicom files
for this dataset or the scan log.
Sita.
On Wed, 9 Jun 2010, Dave Brohawn wrote:
>
Hi Elise,
can you try renaming the file Wedges6_r1_D10_0_pi3_1#0_Coef.nii without
the special character # and rerun mri_vol2surf.
And regarding your second question, what was your command line. Were you
trying to apply the transform talairach.xfm to a volume opened in tkmedit.
Sita.
On Thu,
r the above occurred.***
>
>
> I know that temporal proximity and similar error messages do not necessarily
> mean that the two problems are related, but since they are both happening in
> the same subject's data, it got me wondering.
>
>
> Please let me know if you hav
Hi Ri,
You can try using the dilate and erode label tool in tksurfer.
Click on subject Y's label and in the tksurfer tools window,
Tools -> Labels -> Dilate Selected Label
Tools -> Labels -> Erode Selected Label
Sita.
On Sun, 10 Oct 2010, Ritobrato Datta wrote:
> Hello All,
>
> I hand drew
Hi Forrest,
You can probably try running
recon-all -make all -s
and see if that fixes the problem.
Sita.
On Sun, 3 Apr 2011, Forrest Sheng Bao wrote:
> hi all,
>
> I encountered a strange problem today. I used
>
> recon-all -all
>
> to get surfaces of a subject. I have no problem with his
Hi Allie,
This probably needs white matter edits but it's hard to tell
from one slice. Please refer to our white
matter edits wiki and toplogical defects wiki and see if it helps in
fixing the errors in your datasets. Also it looks like part of the
Cerebellum is stripped off. You might want t
Hi Ri,
I think you can use mri_cor2label with flag --id set to 1.
Sita.
On Mon, 16 May 2011, Ritobrato Datta wrote:
> Hello All,
>
> How do I convert an .mgh file (my .mgh file is a binary mask) onto a label ?
> Is there an automated way other than drawing ?
>
> Thanks
>
> Ri
>
Hi Jeanette,
Which version of FreeSurfer are you running.
Also, can you try renaming the qdec.Qdecrc to .Qdecrc and try again.
Here's more info on editing the .Qdecrc file with the new measures.
https://surfer.nmr.mgh.harvard.edu/fswiki/.Qdecrc
Sita.
On Mon, 13 Jun 2011, Jeanette Berberich w
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