[Freesurfer] Segmentation using Free Surfer.
Hello Free surfer Expert, I have started working on Free surfer. Now i m facing two issues such as : 1. I m trying to use contour ... but it is working as per guidance in website given. https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewTools/VoxelEdit Under heading of Contour Drawcan any tell me pre requisite to draw contour. I have loaded T1 image and then made new volumeafter tat ctrl+alt+ left clicknot working...? Can any one help me with contour function, how to use in details. 2. I wanted to do segmentation of image into WM,GM and CSF. Please suggest what the best way/ Algorithm to so get MRI image segmentation using Freesurfer. Thanks in advance. cheers Saurabh Thakur, ___ 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.
[Freesurfer] Can -min_border_white and -min_gray_at_white_border be edited for single subject in a large group of subjects?
Dear Freesufers, I am trying to understand what happens if I go in and edit the numbers for -min_border_white -min_gray_at_white_border in a single subjects in a large group. Generally we aim to set everything identical when running a group of subjects in FS. I went in and had a look at the recon-all log file and I can see that the numbers for -min_border_white -min_gray_at_white_border different for different subjects. Thus - what will happened if I go and edit the -min_border_white -min_gray_at_white_border numbers for a single subjects in a large bach will I still be able compare cortical thickness with subjects that I did not edit? Or is it necessary to keep the number identical for all subjects when editing the min_border_white -min_gray_at_white_border ___ 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.
Re: [Freesurfer] Number of pixel count
Hi Saurabh we don't measure sulcal CSF as it's really not visible on only a T1. The other measures should all be in the files in the stats directory - no need to measure it yourself. cheers Bruce On Wed, 12 Feb 2014, Saurabh Thakur wrote: Hello Free surfer Expert , I am kooking for the exact value of voxel / pixel which represent White ,Grey and CSF fluid matter in brain. I am trying to draw contour, and to measure the count...or How to count the pixel for particular region...? Thanks in advance for your timely advise. cheers Saurabh Thakur, ___ 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.
Re: [Freesurfer] Segmentation using Free Surfer.
Hi Saurabh have you run recon-all on your subjects? If so, you should be all set (see my previous email) cheers Bruce On Wed, 12 Feb 2014, Saurabh Thakur wrote: Hello Free surfer Expert, I have started working on Free surfer. Now i m facing two issues such as : 1. I m trying to use contour ... but it is working as per guidance in website given. https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewTools/Voxel Edit Under heading of Contour Drawcan any tell me pre requisite to draw contour. I have loaded T1 image and then made new volumeafter tat ctrl+alt+ left clicknot working...? Can any one help me with contour function, how to use in details. 2. I wanted to do segmentation of image into WM,GM and CSF. Please suggest what the best way/ Algorithm to so get MRI image segmentation using Freesurfer. Thanks in advance. cheers Saurabh Thakur, ___ 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.
Re: [Freesurfer] Can -min_border_white and -min_gray_at_white_border be edited for single subject in a large group of subjects?
Hi Erik is there a reason not to do it for the whole group? I guess if the one subject you uploaded had significant motion (which caused the blurryness) then it might be the case that it needs separate parameters. In general though it's good to hold this kind of thing constant as it will definitely bias you to having greater thickness. Try it on some of the other subjects and see if the surfaces are at least as accurate as without, and if so do it uniformly cheers Bruce On Wed, 12 Feb 2014, Erik Lindberg wrote: Dear Freesufers, I am trying to understand what happens if I go in and edit the numbers for -min_border_white -min_gray_at_white_border in a single subjects in a large group. Generally we aim to set everything identical when running a group of subjects in FS. I went in and had a look at the recon-all log file and I can see that the numbers for -min_border_white -min_gray_at_white_border different for different subjects. Thus - what will happened if I go and edit the -min_border_white -min_gray_at_white_border numbers for a single subjects in a large bach will I still be able compare cortical thickness with subjects that I did not edit? Or is it necessary to keep the number identical for all subjects when editing the min_border_white -min_gray_at_white_border ___ 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.
Re: [Freesurfer] Can -min_border_white and -min_gray_at_white_border be edited for single subject in a large group of subjects?
Hi Erik yes, those numbers are always estimated from the data unless you specify otherwise. And please remember to cc the list so that others can answer/see the answers in case they are interested in the same type of issue. cheers Bruce On Wed, 12 Feb 2014, Erik Lindberg wrote: OK Thanks - I suspected that. What made me a bit confused what that I went in and had a look at the recon-all log file. And numbers from this file was different for different subjects at the same batch. two subjects setting MIN_GRAY_AT_WHITE_BORDER to 67.9 (was 70) setting MAX_BORDER_WHITE to 107.3 (was 105) setting MIN_BORDER_WHITE to 79.0 (was 85) setting MAX_CSF to 56.7 (was 40) setting MAX_GRAY to 94.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 73.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 45.6 (was 40) setting MIN_GRAY_AT_WHITE_BORDER to 71.5 (was 70) setting MAX_BORDER_WHITE to 108.1 (was 105) setting MIN_BORDER_WHITE to 82.0 (was 85) setting MAX_CSF to 61.0 (was 40) setting MAX_GRAY to 95.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 76.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 50.5 (was 40) On Wed, Feb 12, 2014 at 2:31 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Erik is there a reason not to do it for the whole group? I guess if the one subject you uploaded had significant motion (which caused the blurryness) then it might be the case that it needs separate parameters. In general though it's good to hold this kind of thing constant as it will definitely bias you to having greater thickness. Try it on some of the other subjects and see if the surfaces are at least as accurate as without, and if so do it uniformly cheers Bruce On Wed, 12 Feb 2014, Erik Lindberg wrote: Dear Freesufers, I am trying to understand what happens if I go in and edit the numbers for -min_border_white -min_gray_at_white_border in a single subjects in a large group. Generally we aim to set everything identical when running a group of subjects in FS. I went in and had a look at the recon-all log file and I can see that the numbers for -min_border_white -min_gray_at_white_border different for different subjects. Thus - what will happened if I go and edit the -min_border_white -min_gray_at_white_border numbers for a single subjects in a large bach will I still be able compare cortical thickness with subjects that I did not edit? Or is it necessary to keep the number identical for all subjects when editing the min_border_white -min_gray_at_white_border 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. ___ 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.
[Freesurfer] distribute dots on the surface
Dear Freesurfers, I have run recon-all and got a set of surfaces for the subjects. I wish to distribute N dots about evenly on the surface to cover most gyri and sulci , but I don't how to implement that. One way is to manually put them in the GUI of freeview, but it is not so convenient if N is relative large (say, 200). Can anyone give me a hint which function shall I use? best Peng ___ 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.
Re: [Freesurfer] distribute dots on the surface
what do you mean by dots? Eg, a mask surface overlay with 1s in some vertices and 0s in others? Or a label? doug On 2/12/14 9:52 AM, peng wrote: Dear Freesurfers, I have run recon-all and got a set of surfaces for the subjects. I wish to distribute N dots about evenly on the surface to cover most gyri and sulci , but I don't how to implement that. One way is to manually put them in the GUI of freeview, but it is not so convenient if N is relative large (say, 200). Can anyone give me a hint which function shall I use? best Peng ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
[Freesurfer] freesurfer course
Hello, I am interested in attending a freesurfer course at Martinos Center for Biomedical Imaging in Bostonhttp://maps.google.com/maps?q=%22114%20Sixteenth%20Street,%20Charlestown,%20MA%2002129%22 But, it says that the following lectures are only during spring and fall. 1)Functional analysis (during the Spring course) 2)Diffusion processing (during the Fall course) I would like to attend the course which covers the above topics. Can you please give me the link for the details of the workshop which includes diffusion and functional course. Regards Jay ___ 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.
[Freesurfer] How to avoid tumour from being segmented out
Hi there, I am creating surfaces from my volume T1-weight scans so that I can run them in AFNI's SUMA program. Problem is that my tumour has been segmented out because its intensity and the intensity of its surround area is much lower that what is being segmented. How can I avoid this? Or edit this? I need my functional MRI data to be displayed around the tumour region which is now unfortunately cut out. (HELPP!!!) Thanks, Melanie Morrison ___ 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.
Re: [Freesurfer] dt_recon error for Siemens mosaics image
has it been anonymized? On 02/11/2014 02:23 PM, Gennan Chen wrote: HI! All, I got an error when I ran dt_recon WARNING: file /Users/gnchen/tmp/3011_DTI/orig/MR01.dcm does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I can confirm it is Siemens mosaics format. Any idea how to by pass this?? -- Gennan Chen This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator ___ 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/ ___ 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.
Re: [Freesurfer] How to avoid tumour from being segmented out
Hi Melanie you should be able to fill it in in the wm.mgz volume in either tkmedit or freeview (using 255 if in freeview - tkmedit will do this by default) cheers Bruce On Wed, 12 Feb 2014, Melanie Morrison wrote: Hi there, I am creating surfaces from my volume T1-weight scans so that I can run them in AFNI's SUMA program. Problem is that my tumour has been segmented out because its intensity and the intensity of its surround area is much lower that what is being segmented. How can I avoid this? Or edit this? I need my functional MRI data to be displayed around the tumour region which is now unfortunately cut out. (HELPP!!!) Thanks, Melanie Morrison ___ 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.
[Freesurfer] Postdoc - ICM Paris - Morphometry using 7T MRI
Dear colleagues, Our team is looking for a postdoctoral fellow. Please find below the informations about the position. Many thanks Olivier Colliot _*Research topic: Computational anatomy of the hippocampus using very high resolution MRI at 7 Tesla: diffeomorphic registration and shape analysis *_The hippocampus is an anatomical structure of the brain which plays critical roles in different brain disorders including Alzheimer's disease and epilepsy. The hippocampus has the particularity of presenting a highly complex tridimensional organization with a large number of substructures, fields and layers. Current approaches for shape analysis of the hippocampus only consider its external boundary and do not model its complex internal architecture. Indeed, using conventional MRI at 1.5T or 3T, only the external boundaries of the hippocampus can be visualized and its internal subregions remain inaccessible. The advent of ultra-high field MRI (7T and higher) has opened new perspectives by providing increased signal-to-noise ratio, increased tissular contrast and increased spatial resolution, which allows visualizing in vivo tiny anatomical structures (~100-200 microns). New computational anatomy approaches are needed to handle these complex anatomical structures. The aim of this postdoctoral project is to develop new approaches for diffeomorphic registration and shape analysis of the internal structures of the hippocampus using 7T MRI data with very high spatial resolution. The developments will be based on the framework of large diffeomorphic deformations and matching of currents. New developments based on varifolds and functional currents will be performed in order to handle the complex shapes of the internal structures. The work will be done in collaboration with our partners at ENS de Cachan (Alain Trouvé) and Université Paris-Descartes (Joan Glaunès). The developed approaches will be applied to detect subtle alterations in patients with Alzheimer's disease and epilepsy in which 7T MRI has been acquired. These clinical applications will be done in collaboration with our partners at Neurospin, Pitié-Salpêtrière hospital, and University of Minnesota. _*Profile of the candidate *_The ideal candidate should have previous experience in the design of new methods for morphometry, shape analysis or registration of anatomical medical images. However, we will also consider outstanding scientific profiles in the fields of image processing/computer vision, without previous experience of the specific topics mentioned above. _*About the ARAMIS team*_ ARAMIS is a joint research team between CNRS, INRIA, Inserm and UPMC within the Brain and Spine Institute (ICM). The ICM (http://icm-institute.org/menu/foundation/mission?lang=en) is a recently created neuroscience center based in the Pitié-Salpêtrière hospital in Paris, which is the largest adult hospital in Europe and has a long tradition of neuroscience and neurology. The ICM brings together 500 researchers covering the whole field of neuroscience. ARAMIS is the methodological research team of the ICM. It is a multidisciplinary group (electrical engineering, computer science, neurology) with about 30 members. The team aims at designing new mathematical and computational approaches for the analysis of images and signals of the human brain. The key domains of expertise of the team are: i) automatic segmentation of brain structures; ii) shape analysis and longitudinal modeling; iii) machine learning; iv) analysis of brain connectivity. The team has developed advanced methods for the analysis of anatomical and functional neuroimaging data including the fully automatic approach SACHA to segment the hippocampus and the amygdala, pattern classification algorithms, the Deformetrica software for shape analysis, and graph-theory approaches to functional connectivity. The team also has strong expertise in the management of multi-center neuroimaging studies, including multi-site MRI harmonization, quality control and analysis of massive datasets. The team has close and enduring collaborations with different clinical teams of the ICM and the Pitié-Salpêtrière hospital to apply advanced image analysis approaches to neurological disorders, including Alzheimer's disease, epilepsy, fronto-temporal dementia, Parkinson's disease, Gilles de la Tourette syndrome. _*Contact information*_ Olivier Colliot - olivier.coll...@upmc.fr - http://cogimage.dsi.cnrs.fr/perso/colliot/ _*More information:*_ https://www.inria.fr/en/institute/recruitment/offers/post-doctoral-research-fellowships/post-doctoral-research-fellowships/campaign-2014/(view)/details.html?id=PNGFK026203F3VBQB6G68LOE1ContractType=4546LG=ENResultsperpage=20nPostingID=8265nPostingTargetID=13985option=52sort=DESCnDepartmentID=19 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
[Freesurfer] Running a template through recon-all
Dear FreeSurfer experts, I am trying to map volumetric ROIs obtained from VBM to surfaces in 5-6 year old children. I saw in a couple previous posts that it is recommended to run the template brain through recon-all, map the ROIs to the template surface, and then propagate the ROIs to all subjects using either mri_surf2surf, or (after turning the ROIs into labels) using mri_label2label. The problem I have is that we used a custom age-appropriate template that will not pass through recon-all. I have tried using -notalairach -notal-check. Here is the output from the recon-all.log: register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 117 -- 126 resetting gm mean[0]: 74 -- 74 input volume #1 is the most T1-like using real data threshold=24.0 skull bounding box = (128, 99, 138) -- (128, 154, 185) using (128, 117, 162) as brain centroid... mean wm in atlas = 126, using box (128,110,156) -- (127, 123,167) to find MRI wm WARNING: gca.c::GCAhistoScaleImageIntensities: h_mri-nbins=255, mri_peak=-1 before smoothing, mri peak at 0 WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri-nbins=255, mri_peak=-1 after smoothing, mri peak at 0, scaling input intensities by inf Linux rc-twice 3.2.21-mosix #1 SMP Mon Jul 2 08:55:48 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s TOM_5yr_2 exited with ERRORS at Mon Feb 10 19:11:23 EST 2014 I am using version 5.3. Can you suggest any other options to get this template through recon-all? Thanks in advance, Danielle ___ 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.
Re: [Freesurfer] dt_recon error for Siemens mosaics image
Possible. Can you give me DICOM tag/tags the program looks for?? Gen -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, February 12, 2014 8:24 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] dt_recon error for Siemens mosaics image has it been anonymized? On 02/11/2014 02:23 PM, Gennan Chen wrote: HI! All, I got an error when I ran dt_recon WARNING: file /Users/gnchen/tmp/3011_DTI/orig/MR01.dcm does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I can confirm it is Siemens mosaics format. Any idea how to by pass this?? -- Gennan Chen -- -- This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator ___ 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/ ___ 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. This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Fwd: Problems dipslaying annotations in freeview
Hi Ruopeng and freesurfer folks, I am still having trouble loading annotations in freeview, similar to what I mentioned before. When I load 'rh.aparc.a2009s.annot' in freeview, the annotation loads onto the LEFT hemisphere and is tye-died in appearance. In contrast, 'lh.aparc.a2009s.annot' loads correctly onto the left hemisphere and looks normal. I have had this problem with many of my subjects. Can you help with this?? Thank you, Laura -- Forwarded message -- Date: Thu, Jan 2, 2014 at 9:53 AM Subject: Fwd: [Freesurfer] Problems dipslaying annotations in freeview To: rpw...@nmr.mgh.harvard.edu Hi Ruopeng, I am forwarding the messages I sent to the freesurfer mailing list and that Doug suggested I ask you. Basically when I try and load an annotation in freeview, the rh loads properly (looks normal and is on the correct hemisphere), but the lh loads onto the rh and is tye-died in appearance. Can you help with this? Thanks, Laura -- Forwarded message -- From: Douglas N Greve gr...@nmr.mgh.harvard.edu Date: Wed, Dec 18, 2013 at 2:14 PM Subject: Re: [Freesurfer] Problems dipslaying annotations in freeview Cc: freesurfer@nmr.mgh.harvard.edu oh, if the lh annot is being loaded onto the rh surface, then that will definitely create the tye-died appearance.* Maybe Ruopeng can weigh in on the freeview issue.* doug On 12/18/2013 04:53 PM, Laura wrote: Hi Douglas, I would go to the annotation drop down menu in freeview, select l/rh.aparc.a2009s.annot and then it would freeze. I can't seem to reproduce that problem today, but for every subject that I load an annotation for now, the rh annotation loads properly,* but the lh annotation loads onto the right hemisphere and is tye-died in appearance.* Thanks, Laura On Tue, Dec 17, 2013 at 11:57 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: So when you say you cannot load it, what do you mean? doug On 12/17/2013 02:55 PM, Laura Taylor wrote: Hi Douglas, I checked the status of each subject once recon-all was completed (by looking in the terminal window before I closed it). Each of my roughly 90 subects had the message /recon-all -s/ subjectID /finished without error/ at date and time. When I look at the recon-all.log file the same message is there at the end. Is there somewhere else where i should look for an error message?? Thank you, Laura On Tue, Dec 17, 2013 at 10:44 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: For the subject that you were not able to load the annot, did you check the recon-all log file? Did recon-all complete properly? doug On 12/17/2013 01:35 PM, Laura wrote: Hi again, Douglas and freesurfer experts. Unfortunately my problem cannot be explained by having made manual edits and then not finishing recon-all. When I load subjects that I did not manually edit, I am either unable to load an annotation file (specifically r/lh.aparc.a2009s.annot) at all, or I can load it but have problems with the output. When I am able to load an image I get a the same tye-died appearing surface for one hemisphere (and it is projected onto the opposite hemisphere that the label is for) or I get a proper surface when I load the label for the other hemisphere (and it appears on the correct hemisphere). Can you help at all with this? Thank you, Laura On Tue, Dec 10, 2013 at 11:45 AM, Laura Taylor wrote: Hi, yes thank you both. That is exactly what the problem was. Laura On Tue, Dec 10, 2013 at 11:12 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Yep, looks like your annot is out of sync with the surfaces On 12/10/2013 01:51 PM, Chris Watson wrote: I've seen this happen after making manual edits and then not finishing a re-run
[Freesurfer] Fwd: How to avoid tumour from being segmented out
Thanks, Melanie Morrison Begin forwarded message: From: Bruce Fischl fis...@nmr.mgh.harvard.edu Date: 12 February, 2014 1:21:56 PM EST To: Melanie Morrison melanie.morri...@hotmail.com Subject: RE: [Freesurfer] How to avoid tumour from being segmented out Hi Melanie can you cc the list so that others can answer? thanks Bruce On Wed, 12 Feb 2014, Melanie Morrison wrote: Thanks. I can just do this manually? Can I over lay this on my anatomical map somehow so I can manually outline the correct boundaries. Date: Wed, 12 Feb 2014 11:51:14 -0500 From: fis...@nmr.mgh.harvard.edu To: melanie.morri...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu; astev...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How to avoid tumour from being segmented out Hi Melanie you should be able to fill it in in the wm.mgz volume in either tkmedit or freeview (using 255 if in freeview - tkmedit will do this by default) cheers Bruce On Wed, 12 Feb 2014, Melanie Morrison wrote: Hi there, I am creating surfaces from my volume T1-weight scans so that I can run them in AFNI's SUMA program. Problem is that my tumour has been segmented out because its intensity and the intensity of its surround area is much lower that what is being segmented. How can I avoid this? Or edit this? I need my functional MRI data to be displayed around the tumour region which is now unfortunately cut out. (HELPP!!!) Thanks, Melanie Morrison ___ 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. ___ 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.
Re: [Freesurfer] local_gi problem
Hi Krista, Try using the following command: tksurfer BV2 lh inflated -overlay $SUBJECTS_DIR/BV2/surf/lh.pial_lgi -fthresh 1 The error you got is because the overlay needs the full path to the pial_lgi file. Then, not all regions are coloured because the default minimum threshold is 2, and you want to set it at 1 to see whether everything want fine (fthresh option). If it's just for quality check it should not be a problem to transfer your subjects from one platform to another. Hope it helps, Marie On Feb 12, 2014, at 9:50 AM, krista kelly krista.kell...@gmail.com wrote: Hello, I am trying to do local gyrification with freesurfer and am having trouble. I have the image processing toolbox and have set the path. I ran recon-all -s BV21 -localGI and it exited without errors. Yet, when I try to view it in tksurfer using tksurfer BV21 lh inflated -overlay lh.pial_lgi, I get this error: cannot find rh.pial_lgi (even though it is in the surfs folder). I can open the inflated brain in tksurfer and overlay lh.pial_lgi but there seems to be a problem where not all of the brain is colored in (please see attached pictures). I'm wondering if someone can help me with this problem, it's happened on more than one participant. When checking through the terminal, I found this at the beginning of the processing: INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 I initially did recon-all -all using a linux on a virtual machine, however there wasn't enough working memory to do all of my analyses using linux, so I transferred all of my data to a mac and did the quality checks, extracted roi data (aparcstats2table) and ran glm analyses (qdec) from there. Do you think that the problem lies in the fact that recon-all was originally ran in Linux? I'd rather not do the local gyrification in Linux as I do not have matlab on that machine. Thanks! Krista Screen Shot 2014-02-12 at 12.49.23 PM.pngScreen Shot 2014-02-12 at 12.49.18 PM.png___ 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Fwd: How to avoid tumour from being segmented out
Hi Melanie doing it in tkmedit (or freeview) would be doing it manually. But if you do it this way it should allow you to correct the resulting surfaces and such cheers Bruce On Wed, 12 Feb 2014, Melanie Morrison wrote: Thanks,Melanie Morrison Begin forwarded message: From: Bruce Fischl fis...@nmr.mgh.harvard.edu Date: 12 February, 2014 1:21:56 PM EST To: Melanie Morrison melanie.morri...@hotmail.com Subject: RE: [Freesurfer] How to avoid tumour from being segmented out Hi Melanie can you cc the list so that others can answer? thanks Bruce On Wed, 12 Feb 2014, Melanie Morrison wrote: Thanks. I can just do this manually? Can I over lay this on my anatomical map somehow so I can manually outline the correct boundaries. Date: Wed, 12 Feb 2014 11:51:14 -0500 From: fis...@nmr.mgh.harvard.edu To: melanie.morri...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu; astev...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How to avoid tumour from being segmented out Hi Melanie you should be able to fill it in in the wm.mgz volume in either tkmedit or freeview (using 255 if in freeview - tkmedit will do this by default) cheers Bruce On Wed, 12 Feb 2014, Melanie Morrison wrote: Hi there, I am creating surfaces from my volume T1-weight scans so that I can run them in AFNI's SUMA program. Problem is that my tumour has been segmented out because its intensity and the intensity of its surround area is much lower that what is being segmented. How can I avoid this? Or edit this? I need my functional MRI data to be displayed around the tumour region which is now unfortunately cut out. (HELPP!!!) Thanks, Melanie Morrison ___ 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] dt_recon error for Siemens mosaics image
It is looking for information in the Siemens ascii header. This is a bit of ascii text that gets stored in a private field in the dicom, but because it is ascii we can just parse the file. It uses this information to determine the size of the mosaic. doug On 02/12/2014 12:23 PM, Gennan Chen wrote: Possible. Can you give me DICOM tag/tags the program looks for?? Gen -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, February 12, 2014 8:24 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] dt_recon error for Siemens mosaics image has it been anonymized? On 02/11/2014 02:23 PM, Gennan Chen wrote: HI! All, I got an error when I ran dt_recon WARNING: file /Users/gnchen/tmp/3011_DTI/orig/MR01.dcm does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I can confirm it is Siemens mosaics format. Any idea how to by pass this?? -- Gennan Chen -- -- This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator ___ 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/ ___ 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. This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator -- 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/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] bbregister and fnirt
Hi all, We're conducting the registration using bbregister that gives us a registration matrix (a .dat file) BUT the original structural file remains intact, i.e. the registered output can be viewed but not stored. Can we store the co-registered structural image as a .nii file? And if so, how? We are using the Connectivity Toolbox that requires structural data to be coregistered with functional data, and there is no way we can feed in the .dat file. Also, what are your thoughts on first using bbregister for linear coregistration, and then use fnirt on the output to get nonlinear coregistration? We ask this because we are working on a younger population (ages 8-25) with autism spectrum disorder and the data is affected by motion. Should we also be using --init-fsl instead of --init-spm if we want to use fnirt? Thank you for your help, Trang ___ 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.
Re: [Freesurfer] Compute DTI metrics in NAWM in Tracula
Hi Anastasia Thanks a lot for your very nice talk today. I would have another question on top of the one below. I have looked at the formula to calculate the total motion index, and for the third motion parameter (percentage of slice with signal drop-out), all subjects except 2 had a 0 value. So in the formula, I would not be able to calculate the motion factor for this parameter because median, upper and lower quartile are all 0, is that correct (it would make (x-0/0-0))? Thanks for your help Celine Hi Anastasia and freesurfer experts, I am trying to get DTI values along the tracts as in the pathstatbyvoxel file, but excluding inflammatory WM lesions. I have masks of the WM lesions that I could apply on the DTI maps, but then how could I compute the DTI metrics along the tract with the exclusion of the lesion? (I guess the last step of trac-all -path could be applied to DTI maps that were masked by the lesions?) I would like to keep the advantage of having the DTI weighted metrics in particular. Thanks a lot for your help! Celine -- Celine Louapre, MD-PhD, Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
Re: [Freesurfer] Tracula version and download problem
Hi Clive - So you are talking about the overall tract stats, averaged over the whole tract (and not the stats by position on the tract that trac-all -stat outputs). That phrase in the tutorial is not very clear - these could be used as a covariate in mri_glmfit, but the main input of mri_glmfit is on a surface or volume. These stats (e.g., average FA of the uncinate fasciculus) are only one value per subject. Hope this helps, a.y On Tue, 11 Feb 2014, Clive Wong wrote: Thanks Anastasia. I ask that because in the tracula stat page, it saids Measures can be extracted from these files to be analyzed further, e.g., for tract-based group analysis. Specifically, the text files can be converted into a table using the command tractstats2table and then used for doing GLM analyses with mri_glmfit or any other statistical software (SPSS, Excel, Statview etc.). So I think I may reuse the GLM matrix. Best, Clive On Tue, Feb 11, 2014 at 8:29 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Clive - These are not stats in the volume or on the surface, so mri_glmfit doesn't apply. If you want to do group analyses along a tract on a table produced by trac-all -stat, you should import the table in any software that you use for statistics (matlab, SPSS, etc). Best, a.y On Mon, 10 Feb 2014, Clive Wong wrote: Dear Anastasia, Thanks very much. I have already downloaded the file. The wiki page was also down a few hours ago, but it's ok now. And I am interested in the tracula group stat. How could I use mri_glmfit on the text file? And can I use the QDEC (or the contrast generated by QDEC) to do the glm? Thanks Clive On Mon, Feb 10, 2014 at 6:13 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Clive - Yes, you can use the recent tracula update on top your already processed data. The new update only adds new functionality to trac-all, without changing any of the existing functionality in 5.3. Did you try downloading the update from here? http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates a.y On Sun, 9 Feb 2014, Clive Wong wrote: Hi, I just want to confirm, is that I can use the new trac-all with the data processed in the original FS5.3 trac-all? And, I just want to download the new trac-all, but I have problem to connect to the ftp server. I can login to the server, but it does not response to any command. Please advise. Best, Clive 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. ___ 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.
Re: [Freesurfer] Fwd: Tracula Error: bvecs and bvals don't have the same number of entries
Ciao Francesco - Just to clarify, to be able to have your bvecs/bvals in rows, you should have, in addition to the latest version of freesurfer, the update that I linked to below: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates a.y On Tue, 11 Feb 2014, Francesco Baldacchini wrote: Ciao Anastasia, I checked and I'm using the latest version of Freesurfer, version 5.3.0. It seems like that the command trac-all path while working on the bvecs table and doing the corrections makes some errors and you can see it from the bvecs file I found in the dmri directory which is only 4 rows long. 2014-02-06 1:18 GMT+01:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Francesco - Which version of tracula are you running? To be able to use bvecs files that are in 3 rows instead of 3 columns, you need to make sure that you have the latest update to tracula, see here: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates This option was not available in the previous releases of tracula. Hope this helps, a.y On Mon, 20 Jan 2014, Francesco Baldacchini wrote: Hi, Sorry Anastasia, I'm seeing that my question was not so clear. The files I sent you in the first mail are the bvecs and bvals saved by trac-all -prep in the dmri directory. The original files are in attachment in this mail, Francesco Baldacchini 2014/1/13 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Hi Francesco - The bvecs file that you're attaching has only 3 vectors, while the bvals file has 65 b-values. Are these your original files, or the ones saved by trac-all in the dmri/ directory? a.y On Mon, 13 Jan 2014, Francesco Baldacchini wrote: Hi everybody, I'm trying to run the trac all -prep command but after some times I get this error bvecs and bvals don't have the same number of entries. I've checked my bvals and bvecs, which are in attach, but they seems to be formatted in the right way. What can I do? Thanks, Francesco Baldacchini 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. ___ 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.
Re: [Freesurfer] Tracula version and download problem
Dear Anastasia, Thank you very much for the clarification. Best, Clive On Thu, Feb 13, 2014 at 8:52 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Clive - So you are talking about the overall tract stats, averaged over the whole tract (and not the stats by position on the tract that trac-all -stat outputs). That phrase in the tutorial is not very clear - these could be used as a covariate in mri_glmfit, but the main input of mri_glmfit is on a surface or volume. These stats (e.g., average FA of the uncinate fasciculus) are only one value per subject. Hope this helps, a.y On Tue, 11 Feb 2014, Clive Wong wrote: Thanks Anastasia. I ask that because in the tracula stat page, it saids Measures can be extracted from these files to be analyzed further, e.g., for tract-based group analysis. Specifically, the text files can be converted into a table using the command tractstats2table and then used for doing GLM analyses with mri_glmfit or any other statistical software (SPSS, Excel, Statview etc.). So I think I may reuse the GLM matrix. Best, Clive On Tue, Feb 11, 2014 at 8:29 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Clive - These are not stats in the volume or on the surface, so mri_glmfit doesn't apply. If you want to do group analyses along a tract on a table produced by trac-all -stat, you should import the table in any software that you use for statistics (matlab, SPSS, etc). Best, a.y On Mon, 10 Feb 2014, Clive Wong wrote: Dear Anastasia, Thanks very much. I have already downloaded the file. The wiki page was also down a few hours ago, but it's ok now. And I am interested in the tracula group stat. How could I use mri_glmfit on the text file? And can I use the QDEC (or the contrast generated by QDEC) to do the glm? Thanks Clive On Mon, Feb 10, 2014 at 6:13 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Clive - Yes, you can use the recent tracula update on top your already processed data. The new update only adds new functionality to trac-all, without changing any of the existing functionality in 5.3. Did you try downloading the update from here? http://surfer.nmr.mgh.harvard. edu/fswiki/Tracula#Updates a.y On Sun, 9 Feb 2014, Clive Wong wrote: Hi, I just want to confirm, is that I can use the new trac-all with the data processed in the original FS5.3 trac-all? And, I just want to download the new trac-all, but I have problem to connect to the ftp server. I can login to the server, but it does not response to any command. Please advise. Best, Clive 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. ___ 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.
Re: [Freesurfer] Fwd: Tracula Error: bvecs and bvals don't have the same number of entries
Hi Francesco - The decimal separator should be dot, not comma. Can you send me the bvecs/bvals that you get after you change from row to column format? (Both the ones that you feed into trac-all and the ones that get created under dmri/.) Thanks, a.y On Tue, 11 Feb 2014, Francesco Baldacchini wrote: Hi again Anastasia, I tried also to convert my three row bvecs file in a three column one but I still got the same bvecs and bvals don't have the same number of entries error. I then tried also to change the dot to comma as the decimal separator but still nothing Francesco Baldacchini 2014-02-11 15:06 GMT+01:00 Francesco Baldacchini frankb...@gmail.com: Ciao Anastasia, I checked and I'm using the latest version of Freesurfer, version 5.3.0. It seems like that the command trac-all path while working on the bvecs table and doing the corrections makes some errors and you can see it from the bvecs file I found in the dmri directory which is only 4 rows long. 2014-02-06 1:18 GMT+01:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Francesco - Which version of tracula are you running? To be able to use bvecs files that are in 3 rows instead of 3 columns, you need to make sure that you have the latest update to tracula, see here: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates This option was not available in the previous releases of tracula. Hope this helps, a.y On Mon, 20 Jan 2014, Francesco Baldacchini wrote: Hi, Sorry Anastasia, I'm seeing that my question was not so clear. The files I sent you in the first mail are the bvecs and bvals saved by trac-all -prep in the dmri directory. The original files are in attachment in this mail, Francesco Baldacchini 2014/1/13 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Hi Francesco - The bvecs file that you're attaching has only 3 vectors, while the bvals file has 65 b-values. Are these your original files, or the ones saved by trac-all in the dmri/ directory? a.y On Mon, 13 Jan 2014, Francesco Baldacchini wrote: Hi everybody, I'm trying to run the trac all -prep command but after some times I get this error bvecs and bvals don't have the same number of entries. I've checked my bvals and bvecs, which are in attach, but they seems to be formatted in the right way. What can I do? Thanks, Francesco Baldacchini 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. ___ 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.
Re: [Freesurfer] Variability in bedpostx output
Hi Jeff - Questions about bedpostx output files are best addressed to the FSL list, as it's an FSL program that is not developped by us. The appropriate info to provide them is the FSL (rather than freesurfer) version numbers. a.y On Tue, 11 Feb 2014, jwa...@nmr.mgh.harvard.edu wrote: Hello all, I have run bedpostx on a series of DTI scans over ~1 year, the earlier ones in stable 5.1 and later ones in 5.3. I'm seeing quite a lot of variability in intensity from the earlier to later versions - re-running bedpostx in 5.3 on an older scan and comparing with 5.1 yields up to 10% variation in intensity at any given voxel between versions. I've been comparing the mean_f1 images by subtracting the (new - old) using fslmaths. The differences are not isolaed to surfaces, but can also be deep in the white matter or parenchyma. Has anyone else seen this? Thanks, Jeff ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
Re: [Freesurfer] Compute DTI metrics in NAWM in Tracula
Hi Celine - That's an interesting question. There's nothing implemented in there right now that would allow you to skip part of the tract in the along-the-tract stats. One (not very elegant) way to try to do something like this is: 1. Set the lesion voxels in the dmri/dtifit_FA.nii.gz volume to zero. (You'll want to save the original volume under some other name for backup first.) If you want the same for the diffusivities, repeat for the also for the MD, L1, L2, L3 volumes. 2. Run the dmri_pathstats command line that you'll find in trac-all.log for that subject. This will regenerate all the pathstats.* files, but now the parts of the tract that go through the lesions will have zero values (or very low, if they're mixed in with some neighboring voxels). Let us know if this worked! If not I may be able to implement something. a.y On Tue, 11 Feb 2014, Celine Louapre wrote: Hi Anastasia and freesurfer experts, I am trying to get DTI values along the tracts as in the pathstatbyvoxel file, but excluding inflammatory WM lesions. I have masks of the WM lesions that I could apply on the DTI maps, but then how could I compute the DTI metrics along the tract with the exclusion of the lesion? (I guess the last step of trac-all -path could be applied to DTI maps that were masked by the lesions?) I would like to keep the advantage of having the DTI weighted metrics in particular. Thanks a lot for your help! Celine ___ 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.
Re: [Freesurfer] Compute DTI metrics in NAWM in Tracula
Celine - You're very welcome! If this particular motion measure is identical for pretty much all your subjects, there is no point in including it. So you can just use the other 3 motion measures. a.y On Wed, 12 Feb 2014, Celine Louapre wrote: Hi Anastasia Thanks a lot for your very nice talk today. I would have another question on top of the one below. I have looked at the formula to calculate the total motion index, and for the third motion parameter (percentage of slice with signal drop-out), all subjects except 2 had a 0 value. So in the formula, I would not be able to calculate the motion factor for this parameter because median, upper and lower quartile are all 0, is that correct (it would make (x-0/0-0))? Thanks for your help Celine Hi Anastasia and freesurfer experts, I am trying to get DTI values along the tracts as in the pathstatbyvoxel file, but excluding inflammatory WM lesions. I have masks of the WM lesions that I could apply on the DTI maps, but then how could I compute the DTI metrics along the tract with the exclusion of the lesion? (I guess the last step of trac-all -path could be applied to DTI maps that were masked by the lesions?) I would like to keep the advantage of having the DTI weighted metrics in particular. Thanks a lot for your help! Celine -- Celine Louapre, MD-PhD, Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
Re: [Freesurfer] Variability in bedpostx output
Wow, that's interesting. In both cases it's called with the default settings, without specifying any special options on the command line. You could verify this by running the respective versions of bedpostx independently of tracula and looking at the outputs. Unless of course something has changed with the inputs to bedpostx (so in the pre-processing steps), in which case the differences wouldn't have to do with bedpostx itself. On Wed, 12 Feb 2014, jwa...@nmr.mgh.harvard.edu wrote: Thank you Anastasia. Unfortunately, I posted the question to the FSL list first and after a few go-rounds with clarification and more info, they felt like it was potentially a problem of the calls to the bedposts command from within Freesurfer. Their final assessment was that there should be no differences in output between different versions of bedpostx, so there must be some difference in how stable 5.1 and 5.3 call the command. Can you provide any more details about how 5.1 and 5.3 differ in this way? Thank you, Jeff Hi Jeff - Questions about bedpostx output files are best addressed to the FSL list, as it's an FSL program that is not developped by us. The appropriate info to provide them is the FSL (rather than freesurfer) version numbers. a.y On Tue, 11 Feb 2014, jwa...@nmr.mgh.harvard.edu wrote: Hello all, I have run bedpostx on a series of DTI scans over ~1 year, the earlier ones in stable 5.1 and later ones in 5.3. I'm seeing quite a lot of variability in intensity from the earlier to later versions - re-running bedpostx in 5.3 on an older scan and comparing with 5.1 yields up to 10% variation in intensity at any given voxel between versions. I've been comparing the mean_f1 images by subtracting the (new - old) using fslmaths. The differences are not isolaed to surfaces, but can also be deep in the white matter or parenchyma. Has anyone else seen this? Thanks, Jeff ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
[Freesurfer] recon-all CTABreadASCII error
Dear FS experts, It represents this message in the command window after ran recon-all -autorecon-pial -s CON_EIU01 -no-isrunning: Reading annotation reading colortable from annotation file... colortable with 36 entries read originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) CTABwriteFileASCII(/tmp/mri_segstats.tmp.CON_EIU04.lh.64.ctab): could not open for writing Seg base 1000 Permission denied CTABreadASCII(/tmp/mri_segstats.tmp.CON_EIU04.lh.64.ctab): could not open file No such file or directory ERROR: reading /tmp/mri_segstats.tmp.CON_EIU04.lh.64.ctab Linux centos2 2.6.18-308.20.1.el5xen #1 SMP Tue Nov 13 11:03:56 EST 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s CON_EIU04 exited with ERRORS at Thu Feb 13 14:01:12 CST 2014 Thanks. All the best. Rujing Zha 2014-02-13 charujing123___ 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.
