Re: [Freesurfer] WM error near the right putamen

t as a last resort, is it worth to rerun everything using an earlier version of FS? Thank you. Gabor Gabor Perlaki ezt írta (időpont: 2022. márc. 28., H, 14:55): > Can you please help me with which measures are not valid in this case? Are > the cortical (e.g. thickness of ctx-rh-medialorbitof

Re: [Freesurfer] WM error near the right putamen

. Only the pial seems to be affected. Thank you in advance for your help. Gabor Perlaki ezt írta (időpont: 2022. márc. 26., Szo, 12:56): > Could anybody please help me with this? > > Gabor Perlaki ezt írta (időpont: 2022. márc. > 22., K, 0:31): > >> Dear all, >> >>

Re: [Freesurfer] WM error near the right putamen

External Email - Use Caution Could anybody please help me with this? Gabor Perlaki ezt írta (időpont: 2022. márc. 22., K, 0:31): > Dear all, > > fswiki suggests that " There are regions where the surfaces are not > intended to be accurate that you should b

[Freesurfer] WM error near the right putamen

External Email - Use Caution Dear all, fswiki suggests that " There are regions where the surfaces are not intended to be accurate that you should be aware of: Areas around the hippocampus and amygdala. " I also found inaccuracy of the WM surface near the putamen and accumbens re

[Freesurfer] mritotal for talairach registration in FS7

External Email - Use Caution This email was sent 22 hours ago, but somehow it haven't appeared on the forum yet. I post it again. Gabor Perlaki ezt írta (időpont: 2021. jún. 2., Sze, 12:11): > The default talairach registration is wrong in ~20% of our subjects and >

Re: [Freesurfer] Problem with talairach check in Freesurfer 7

talairach transform in FS7. I'd really-really appreciate any suggestions/workaround to overcome this. Gabor Perlaki ezt írta (időpont: 2021. máj. 19., Sze, 12:50): > I try to describe in more detail my problems with talairach > check/correction in Freesurfer 7. In earlier versions, I

[Freesurfer] Problem with talairach check in Freesurfer 7

as the MOVEABLE volume and the Talairach volume as the TARGET volume, while in tkregister2 I see the subject's volume as the TARGET volume and Talairach volume as a fuzzy MOVEABLE volume. I'd really appreciate any help regarding the above. At present, I can check talairach using tkregister2 as

[Freesurfer] Problem with talairach check in Freesurfer 7

External Email - Use Caution Dear all, I tried to check the talairach transformation under Freesurfer 7 linux version (freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551). However, neither command works as expected. the command "freeview -v bert/mri/T1.mgz -v bert/mri/brainma

Re: [Freesurfer] hippocampal subfield segmentation question

External Email - Use Caution Dear Eugenio, Thank you for the quick help. Best, Gabor ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] hippocampal subfield segmentation question

External Email - Use Caution We have a sagittal 1 mm isotropic whole-brain 3D T1 mprage (morphometry protocol suggested on Freesurfer's page) and a coronal anisotropic (0.4mm inplane, 2mm thickness, similar to ADNI protocol) T2 measurement acquired perpendicular to the hippocampus

Re: [Freesurfer] MRI protocol for hippocampal subfield segmentation

According to Bruce's request I repost the rest of thread: We set up our our hippocampal subfield T2 protocol based on the ADNI protocol (with some minor differences) as suggested by Iglesias. However, we see an artefact similar to the image found in ADNI2 training manual (page 28): http://adni.lon

Re: [Freesurfer] MRI protocol for hippocampal subfield segmentation

Does anybody else have a comment on the experienced artefact ___ 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

Re: [Freesurfer] MRI protocol for hippocampal subfield segmentation

Does anybody else have a comment on the experienced artefact? ___ 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

Re: [Freesurfer] MRI protocol for hippocampal subfield segmentation

Dear Iglesias, We set up our our hippocampal subfield T2 protocol based on the ADNI protocol (with some minor differences). However, we see an artefact similar to the image found in ADNI2 training manual (page 28): http://adni.loni.usc.edu/wp-content/uploads/2012/10/ADNI2MRITrainingManual_2014.pdf

Re: [Freesurfer] MRI protocol for hippocampal subfield segmentation

Dear Iglesias, Do you think that it is useful to also use a fieldmap for hippocampal subfield segmentation? Can Freesurfer's hippocampal subfield segmentation use it? I'm not sure that due to the limited resolution of the fieldmap and due to registration issues it is worth to acquire a fieldmap fo

Re: [Freesurfer] MRI protocol for hippocampal subfield segmentation

field segmentation if I use distortion corrected highresolution T2 TSE and uncorrected T1 MPRAGE images for the evaluation? Thank you in advance, Gabor 2017-12-04 11:19 GMT+01:00 Gabor Perlaki : > I've two questions regarding hippocampal subfield segmentation: > > 1, Is there a

[Freesurfer] MRI protocol for hippocampal subfield segmentation

I've two questions regarding hippocampal subfield segmentation: 1, Is there any article or other document which containes an optimal T2 protocol with detailed sequence parameters for hippocampal subfield segmentation? (eg. BW, echo time, repetition time, FOV, echo train, paralell imaging on/off, .

Re: [Freesurfer] bad midline cut

Dear Bruce, Did you get my email with the link for our problematic data? Best Regards, Gabor ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is in

Re: [Freesurfer] bad midline cut

Dear Bruce, I sent you a link for our subject's data by email. Best regards, Gabor ___ 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

Re: [Freesurfer] bad midline cut

I've already corrected aseg.presurf.mgz and the left and right lateral ventricles are now correct in the final aseg.mgz. However the pial surface is almost the same as earlier: https://mega.nz/#!XAZkWLZa!a6NgkEtiHzEqUkhZ6WimPgUKxytsGHKrgOLfyHdUuEM https://mega.nz/#!XRRHna7Q!vaeSLG5Cv-fGW-0xdEJlgF

Re: [Freesurfer] bad midline cut

If I accurately understand the recon-all script, then -noaseg sets UseAseg=0, but "autorecon2-noaseg" is a different flag, which only sets the following things. case "-autorecon2-cp": case "-autorecon2-noaseg": case "-autorecon2-wm": set DoNormalization2 = 1; set DoSegment

Re: [Freesurfer] bad midline cut

Dear Bruce, >From the recon-all script it seems to me that autorecon2-noaseg, autorecon2-wm and autorecon2-cp are totally equivalent (the same flags are defined to be true in all three cases). Could you confirm this? Best regards, Gabor ___ Freesurfe

Re: [Freesurfer] bad midline cut

Dear Bruce, I've corrected the lateral ventricles in the aseg.presurf.mgz and ran "recon-all -autorecon2-noaseg -autorecon3 -subjid". Although the labels in aseg.mgz is fine the surfaces (and midline cut) remained bad. Any other idea how to correct this type of error? Best Regards, Gabor

Re: [Freesurfer] bad midline cut

I'll try your suggestion. Thank you very much. ___ 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

Re: [Freesurfer] bad midline cut

https://mega.nz/#!XAZkWLZa!a6NgkEtiHzEqUkhZ6WimPgUKxytsGHKrgOLfyHdUuEM https://mega.nz/#!XRRHna7Q!vaeSLG5Cv-fGW-0xdEJlgFTNRPm7qGHOlShYh7y5z1g 2017-09-25 13:50 GMT+02:00 Gabor Perlaki : > Here are links to images showing the bad midline cut. > Could anybody help me how to solve this issu

Re: [Freesurfer] bad midline cut

Here are links to images showing the bad midline cut. Could anybody help me how to solve this issue? The main cause seems to be asymmetric lateral ventricles. Best, Gabor 2017-09-23 8:18 GMT+02:00 Gabor Perlaki : > Dear all, > Here is my question again. Somehow, it didn't ap

[Freesurfer] bad midline cut

Dear all, Here is my question again. Somehow, it didn't appear on the Freesurfer forum. I'm resending it without the attachments. > I've a subject, where the midline cut is bad (see the attached pictures), > therefore the segmented left lateral ventricle also includes considerable > number of vo

[Freesurfer] Fwd: surface inaccuracies around the optic chiasm

Somehow, my last email didn't appear on the Freesurfer forum. I'm resending it without the attachments. Dear Bruce, I'm not interested in the chiasm, but the medialorbitofrontal cortex would be interesting. In most of the subjects pial and white surfaces intrude into the area around the optic chi

[Freesurfer] surface inaccuracies around the optic chiasm

Dear all, I use Freesurfer 6. In some of my subjects the surfaces (both pial and white) intruding into the optic chiasm. However, when I check the aparc.DKTatlas+aseg.mgz it seems that although the surfaces are wrong, the region is segmented as optic chiasm. Can I ignore this type of surface inac

Re: [Freesurfer] DKT vs. DK Freesurfer atlases

used in the article and whether the DKT40 atlas related > results were also created by Freesurfer in the article by Klein and > Tourville? Are the Freesurfer created results in lh.aparc.DKTatlas.stats > generally more reliable than the results in lh.aparc.stats? > > > > -- > Gab

[Freesurfer] DKT vs. DK Freesurfer atlases

n and Tourville? Are the Freesurfer created results in lh.aparc.DKTatlas.stats generally more reliable than the results in lh.aparc.stats? -- Gabor Perlaki research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-30-2084367 E-mail: petzinger.ga...@gmai

[Freesurfer] transform a custom segmentation to native space

Dear all, We've segmented some brain regions on orig.mgz using another program (this custom segmentation is called our_segmentation.mgz). Is it possible to transform this segmentation into the original native anatomical space using the following command? mri_label2vol --seg our_segmentation.mgz -

[Freesurfer] pial surface vs. aparc segmentation inconsistency

Somehow, my earlier post is unvisible on the maillist, therefore I send it again without the attached image. Dear all, In some of our subjects the border of ctx_lh_parahippocampal (green color) is inconsistent with the border of pial surface (red color) in the sense that some small region within

Re: [Freesurfer] Freesurfer longitudinal analysis accuracy

Any suggestion from the authors of Freesurfer about accuracy of longitudinal Freesurfer for the cerebellum in healthy subjects? Best, Gabor 2016-12-06 11:44 GMT+01:00 Gabor Perlaki : > Dear all, > > We've run longitudinal Freesurfer on 30 healthy subjects. We have two >

[Freesurfer] Freesurfer longitudinal analysis accuracy

Dear all, We've run longitudinal Freesurfer on 30 healthy subjects. We have two subgroups (n=15) and we found a significant longitudinal change in the left and right cerebellar cortex in one of our subgroups. However, this change is very small: mean=0.67% range: -1.61-2.3% for the right cerebellar

[Freesurfer] freesurfer longitudinal data

Dear all, Is it possible to get simple ROI data (such as aseg.stats or aparc.stats in case of cross-sectional analysis) as the result of the longitudinal analysis, which can be further analyzed by SPSS? Best Regards, Gabor ___ Freesurfer mailing list F

Re: [Freesurfer] RB_all_2008-03-26.gca

is suboptimal), or it is rather related to some demographic/disease related differences between the training data and our subjects, and/or it is a segmentation algorithm related issue. Best Regards, Gabor 2016-07-14 15:30 GMT+02:00 Gabor Perlaki : > Dear all, > > Is it possible s

[Freesurfer] RB_all_2008-03-26.gca

Dear all, Is it possible somehow to visually inspect the segmentations of the individual subjects used for the RB_all_2008-03-26.gca atlas? I can extract the means, priors and labels, but I am rather interested in the original MRI intensities and labels for the individual subjects. Best Regards,

Re: [Freesurfer] checking freesurfer output

Dear Bruce, Thank you for your answer. We will check the pial and white surfaces, but how to check the accuracy of the cortical parcellation beyond that? We don't find any suggestion on Freesurfer's troubleshooting page how to realize or correct such an error, where the pial and white surfaces are

[Freesurfer] checking freesurfer output

Sorry to repost my question. I would appreciate any reply. Best Regards, Gabor 2016-06-13 10:51 GMT+02:00 Gabor Perlaki : > Dear all, > > I've a lot of patients and we are looking for the fastest solution to > check the output of Freesurfer. On the troubleshooti

[Freesurfer] checking freesurfer output

Dear all, I've a lot of patients and we are looking for the fastest solution to check the output of Freesurfer. On the troubleshooting page ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData) there are a lot of steps to check, but I think not all of that should be done to f

[Freesurfer] Freesurfer volume-based segmentation

Dear all, I'd like to ask which steps are essential to check if I'm interested only in the volume based (aseg) results. I think Skull strip and Talairach transformation are essential. Any other steps I need to check? Thanks, Gabor ___ Freesurfer mailin

[Freesurfer] aparc+aseg.mgz to nifti conversion

Dear all, I'd like to convert the aparc+aseg.mgz to nifti and use it in the space of the original MR image. The basic conversion from mgz to nifti works fine "mri_convert aparc+aseg.mgz aparc+aseg.nii". However if I reslice it in the space of the original MRI than something fails and even negative

Re: [Freesurfer] aseg.stats volume mismatch

Dear Bruce, I think of a probability map for each segmented structure, like the partial volume images for WM, GM and CSF in FSL. Is there anything like that in Freesurfer? Thanks, Gabor 2014-05-09 22:48 GMT+02:00 Gabor Perlaki : > Dear Bruce, > > I think of a file which also shows th

Re: [Freesurfer] aseg.stats volume mismatch

Dear Bruce, I think of a file which also shows the partial volume estimates for the segmented structures. Thanks, Gabor 2014-05-07 22:31 GMT+02:00 Gabor Perlaki : > Dear Bruce, > > Is there a file generated by freesurfer which stores the subcortical > segmentations together with the

Re: [Freesurfer] aseg.stats volume mismatch

Dear Bruce, Is there a file generated by freesurfer which stores the subcortical segmentations together with the information of partial volume estimates? Thanks, Gabor ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harva

[Freesurfer] aseg.stats volume mismatch

Dear all, I've loaded the mri/aseg.mgz in slicer3D and done a label statistics on the image. The left caudate was reported to be 4005 mm^3 and the right caudate to be 4011 mm^3 by Slicer3D. However, these numbers are somewhat different from the values reported in aseg.stats: 3757 mm^3 and 3901 mm^

[Freesurfer] missing Freesurfer wiki pages

Dear all, Most of the links on https://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction page do not work. If I clik for example on FsTutorial/SkullStripFix the following message will popup: "This page does not exist yet. You can create a new empty page, or use one of the page templates.

[Freesurfer] hippocampal subfields

is FOV. Is there any other suggested article to set up our measurements? Thanks, -- Gabor Perlaki ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is inten

[Freesurfer] Subcortical volume stream

Dear all, Is there any commands in Freesurfer, which segment only the subcortical structures for me? The -autorecon2 calculates also the surfaces which seems unnecessary. However, I don't know whether the final surfaces have an effectt on subcortical volumes. There was a question about it on the F

[Freesurfer] aseg.stats vs. volumes in native T1 space

Dear all, I've run the freesurfer on 3 subjects and converted the aseg.mgz into *.nii.gz in the native space: "mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg2raw.nii.gz" I've did a stats on left and right hippocampal volumes in the native space using fslstats: "fslstats aseg2raw.nii.gz -

[Freesurfer] expanding pial surface

hanks, Gabor -- Gabor Perlaki research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-30-4098480 E-mail: petzinger.ga...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/ma

[Freesurfer] TRACULA Question

Dear Anastasia, Earlier I was posted an issue about BA44/pars triangular: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23706.html Because TRACULA also uses the cortical parcellation it may be important to handle this issue somehow. Is it handled in TRACULA analysis? Does it affec

[Freesurfer] Fwd: pars triangular and BA44 segmentation bug?

if it is a real issue, which labels we shouldn't use for statistical analysis. Thank you in advance for your answer, Gabor 2012/6/25 Bruce Fischl > sure. Thanks for pointing out the BA44 issue. We'll put together a fix in > the next couple of weeks > Bruce > > On Mo

Re: [Freesurfer] pars triangular and BA44 segmentation bug?

s will get you a solution > > > On Sat, 23 Jun 2012, Gabor Perlaki wrote: > > Dear Bruce, >> >> We don't used any thresholding by ourselves, we just took BA44 volumes out >> of the text-file in the stats directory. >> Should we use thresholded values in

Re: [Freesurfer] pars triangular and BA44 segmentation bug?

cted area has the > average area of the input labels. The right BA44 had more spatial spread > than the left, so you might be including a lot of low probability vertices. > > cheers > Bruce > > > On Sat, 23 Jun 2012, Gabor Perlaki wrote: > > Dear Bruce, >> >>

Re: [Freesurfer] pars triangular and BA44 segmentation bug?

Dear Bruce, In the paper "Left-right asymmetry in volume and number of neurons in adult Broca's area." by Katrin Amunts, 10 subjects (5 men and 5 women) were studied, and the volume of BA44 was greater in the left hemisphere than in the right in all ten cases. So, it is very strange that the volum

[Freesurfer] how much talairach registration affects segmentation?

Dear all, I've subjects processed by freesurfer 5.1.0. We checked the talairach transformation. It seems to be not so bad, but sometimes the zoom or the roation are not the best, which may affect the TIV, however we're actually not interested in TIV. Does this "talairach transformation issue" aff

[Freesurfer] ICV calculation error?

Hi all, We use freesurfer 5.1.0 and we ran the recon-all on 100 subjects. We checked the talairach transform, skull strip the pial surfaces and the segmentations as suggested on Freesurfer Wiki. Everything seems to be fine, however, the ICV values from the stats/aseg.stats seem to be incorrect. T

Re: [Freesurfer] trac-all -bedp error

Dear Priti The bedpostx works fine on the data if I run it outside of tracula. The command "/home/kutato12/freesurfer/bin/fsl_sub_seychelles -T 60 -m a -N bedpostx_pre -l /home/kutato12/freesurfer/subjects/my_subject/dmri.bedpostX/logs ${FSLDIR}/bin/bedpostx_preproc.sh /home/kutato12/freesurfer/s

[Freesurfer] trac-all -bedp error

Dear all, I've the following error right after starting trac-all -bedp -c configuration_file: Making bedpostx directory structure Queuing preprocessing stages [: 223: NONE: unexpected operator [: 314: NONE: unexpected operator [: 327: xbedpostx_pre: unexpected operator [: 486: x: unexpected opera

Re: [Freesurfer] mri_aparc2aseg error during trac-all

The problem is solved. Somehow the lh.white file was broken during file transfer. 2012/5/22 Gabor Perlaki > Hi all! > > I've just ran the preprocessing for TRACULA analysis, with the command > "trac-all > -prep -c /home/kutato12/Desktop/dmrirc". It works everythin

[Freesurfer] mri_aparc2aseg error during trac-all

Hi all! I've just ran the preprocessing for TRACULA analysis, with the command "trac-all -prep -c /home/kutato12/Desktop/dmrirc". It works everything fine, and the output files are correct until the following command: mri_aparc2aseg --s my_subject --annot aparc --wmparc-dmax 2 --labelwm --hypo-a

Re: [Freesurfer] TRACULA niftii file

inal DICOM files, you can pass those as > the input, too. > > Hope this helps, > a.y > > > On Thu, 10 May 2012, Gabor Perlaki wrote: > > Dear all, >> >> Is TRACULA able to handle 4D FSL niftii as input for DTI images? Are >> bves/bvalues extracted by dcm2n

[Freesurfer] TRACULA niftii file

Dear all, Is TRACULA able to handle 4D FSL niftii as input for DTI images? Are bves/bvalues extracted by dcm2nii and MRICro accurate for TRACULA? I think TRACULA needs the bvecs in the image coordinate system, which is not the same as scanner coordinate system in case of oblique acquisition. Do I

[Freesurfer] Tracula Siemens DTI

Dear Freesurfers, I have DTI images acquired on a Siemens 3T TIM Trio (software version VB17A). 1, Is TRACULA able to extract the correct b-values and b-vectors from the DICOM headers of Siemens IMA files or do I need to specify them? 2, I'm not sure whether the gradient directions are stored in

[Freesurfer] FSL_niftii

Dear all, I've some fsl niftii MPRAGE images converted by MRIConverter. They look fine in fslview and I can open them by freesurfer as well (tkmedit -f *.nii.gz) , but when I compare the images between fslview and tkmedit they look slightly different. It seems that the orientation is the same in b

[Freesurfer] wm_excluded

Dear all, I'm new in freesurfer. I ran "recon-all -all" on 8 subjects without error, and I loaded the wm.mgz and the surfs. White matter surface (yellow line) seems pretty good by visual inspection, but the wm.mgz seems not so good everywhere. There are certain white-matter areas, which are clearl