[Freesurfer] remote access to freesurfer installation...
External Email - Use Caution Hi: Is there a freesurfer facility where an MRI study can be processed remotely? Sincerely, Gonzalo Rojas Costa ___ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] freeview error....
External Email - Use Caution Hi: I have Ubuntu 18.04.4 LTS and freesurfer release freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275. When I run freeview, I got the error: "This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, webgl, xcb." How can I correct it? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] online freesurfer
External Email - Use Caution Hi: Is there a freesurfer-based system that allows processing online an mprage image? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] Longitudinal SAMSEG with multi-contrast data
External Email - Use Caution Hi: How can I generate "tp1_flair_reg.mgz" image appeared in command "run_samseg_long --timepoint tp0_t1_reg.mgz tp0_flair_reg.mgz --timepoint tp1_t1_reg.mgz tp1_flair_reg.mgz --timepoint tp2_t1_reg.mgz tp2_flair_reg.mgz --output outputDir/" ? Sincerely, Gonzalo Rojas Costa ___ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] fsl fmri thresh_zstat1.nii file showing in fsaverage pial surface
External Email - Use Caution Hi: I processed an fMRI task using FSL. I got the standard image coregistered result... How can I show the thresh_zstat1.nii file in fsaverage pial surface? Sincerely, Gonzalo Rojas Costa ___ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] mri_synthseg problem with CT... freesurver v 7.3.2
External Email - Use Caution Hi: I downloaded some CT from OASIS 4 database... I tried to segment it using mri_synthseg (freesurfer v 7.3.2)... But I got bad results... Only I got the segmentation of one region of the brain... Also, I do the crop of the image, and the threshold from 0-80 hounsfield units... Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 ___ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] automatic screenshots to all axial slices
External Email - Use Caution Hi: I need to take screenshots of all axial slices of a volumetric image that I am viewing using freeview (flair with a segmentation). How can I do it automatically? Sincerely, Gonzalo Rojas Costa ___ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] multiple axial slice screenshots
External Email - Use Caution Hi: I need to take screenshots to all axial slices of a volumetric image that I am viewing using freeview (flair with a segmentation). Sincerely, Gonzalo Rojas Costa ___ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] mri_synthseg error...
External Email - Use Caution
Hi:
I installed the 22 march freesurfer developer version. I test
mri_synthseg with a CT image, but it shows me the following error:
"mri_synthseg --i /home/developer/Documents/sub-0001/H2.nii.gz --o
/home/developer/Documents/sub-0001 --cpu --ct
Traceback (most recent call last):
File "/usr/local/freesurfer/7-dev/python/scripts/mri_synthseg", line 22,
in
import tensorflow as tf
File
"/usr/local/freesurfer/7-dev/python/lib/python3.8/site-packages/tensorflow/__init__.py",
line 479, in
keras._load()
File
"/usr/local/freesurfer/7-dev/python/lib/python3.8/site-packages/tensorflow/python/util/lazy_loader.py",
line 45, in _load
module = importlib.import_module(self.__name__)
File
"/usr/local/freesurfer/7-dev/python/lib/python3.8/importlib/__init__.py",
line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File
"/usr/local/freesurfer/7-dev/python/lib/python3.8/site-packages/keras/__init__.py",
line 25, in
from keras import models
File
"/usr/local/freesurfer/7-dev/python/lib/python3.8/site-packages/keras/models/__init__.py",
line 18, in
from keras.engine.functional import Functional
File
"/usr/local/freesurfer/7-dev/python/lib/python3.8/site-packages/keras/engine/functional.py",
line 25, in
from keras.engine import base_layer
File
"/usr/local/freesurfer/7-dev/python/lib/python3.8/site-packages/keras/engine/base_layer.py",
line 43, in
from keras.mixed_precision import loss_scale_optimizer
File
"/usr/local/freesurfer/7-dev/python/lib/python3.8/site-packages/keras/mixed_precision/loss_scale_optimizer.py",
line 20, in
from keras.optimizer_v2 import optimizer_v2
File
"/usr/local/freesurfer/7-dev/python/lib/python3.8/site-packages/keras/optimizer_v2/optimizer_v2.py",
line 36, in
keras_optimizers_gauge = tf.__internal__.monitoring.BoolGauge(
File
"/usr/local/freesurfer/7-dev/python/lib/python3.8/site-packages/tensorflow/python/eager/monitoring.py",
line 360, in __init__
super(BoolGauge, self).__init__('BoolGauge', _bool_gauge_methods,
File
"/usr/local/freesurfer/7-dev/python/lib/python3.8/site-packages/tensorflow/python/eager/monitoring.py",
line 135, in __init__
self._metric = self._metric_methods[self._label_length].create(*args)
tensorflow.python.framework.errors_impl.AlreadyExistsError: Another metric
with the same name already exists."
Which could be the problem ?
Sincerely,
Gonzalo Rojas Costa
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
___
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contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
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[Freesurfer] mri_synthsr with CT images
External Email - Use Caution Dear Juan: I tested mri_synthsr using three different CT images with the threshold (80 value) that you told me some days ago. The first works ok, but with the other 2, I got the following error: developer@developer-VirtualBox:~$ mri_synthseg --i /home/developer/Documents/OAS31367/sub-OAS31367_sess-d0142_run-01_CT_0_80.nii.gz --o /home/developer/Documents/OAS31367 --cpu SynthSeg 2.0 using CPU, hiding all CUDA_VISIBLE_DEVICES using 1 thread predicting 1/1 Killed What does "Killed" mean? Any log file? Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 ___ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] CT and mri_synthsr
External Email - Use Caution Dear Juan: I tested mri_synthsr using three different CT images using the threshold (80 value) that you told me some days ago. The first works ok, but with the other 2, I got the following error: developer@developer-VirtualBox:~$ mri_synthseg --i /home/developer/Documents/OAS31367/sub-OAS31367_sess-d0142_run-01_CT_0_80.nii.gz --o /home/developer/Documents/OAS31367 --cpu SynthSeg 2.0 using CPU, hiding all CUDA_VISIBLE_DEVICES using 1 thread predicting 1/1 Killed What does "Killed" mean? Any log file? Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 ___ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Re: [Freesurfer] SynthSeg with CT images.
External Email - Use Caution Ok... Thanks you very much... Gonzalo Rojas Costa On Wed, Mar 8, 2023 at 5:38 PM Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mgh.harvard.edu> wrote: > I added a flag (--ct) to mri_synthsr in FreeSurfer so people don’t need to > clip manually when they process CT scans. It should be on the publich > development distribution in a couple of days 😉 > > Cheers, > > /E > > > > -- > > Juan Eugenio Iglesias > > http://secure-web.cisco.com/1IR1bx4iIiu483c-gubT-7sJz9-PHRZ1A5blSSl0RB6i-5Oq7Y6VBPrITJ8QUygst9SyCI4T1sIu_QuDmaBHNm5DuRZlMCX0aQHCv0fpUy-Xq4Jy9OD24jYHE-kgGEOvFDWKC8Yx1Zuy5xcuXv-rrVcbeNoSIj8CCrsv2_LqsKLr_V98ORWNt-IKEkjx6j4X6CEVlrOFW5SfiYdOoBU5tQtT1JKc4defdRrJ9PKjkohbxc5hj9LvTrfECL73uLC7ZEiWTP5kc_9x8w-6ruYnZ97LEWX-rjo4bphX2Dp-2cGYk4ifRN1M5yqz27YcONKg6/http%3A%2F%2Fwww.jeiglesias.com > > > > *From: *Gonzalo Rojas Costa > *Date: *Wednesday, March 8, 2023 at 13:56 > *To: *Benjamin Billot > *Cc: *"Iglesias Gonzalez, Juan E." , " > freesurfer@nmr.mgh.harvard.edu" > *Subject: *Re: SynthSeg with CT images. > > > > *External Email - Use Caution* > > Hi Benjamin: > > > > I tested with the clipping, and it works ok with a CT image. > > > > Sincerely > > > > > > Gonzalo Rojas Costa > > > > > > El mié, 8 de mar de 2023, 14:39, Benjamin Billot > escribió: > > Yes, agreed. > > Gonzalo: Also, if SynthSeg still gives you a bad result after clipping, > you might want to check that the image header is not corrupted. > > Best > > Benjamin > -- > > *From:* Iglesias Gonzalez, Juan E. > *Sent:* 08 March 2023 12:25 > *To:* Gonzalo Rojas Costa; freesurfer@nmr.mgh.harvard.edu > *Cc:* Benjamin Billot > *Subject:* Re: SynthSeg with CT images. > > > > Dear Gonzalo, > > Can you please try clipping the input to Hounsfield between 0 and 80? That > should do the trick. If you have trouble with this, feel free to send me > scan so I can take a look. > > Benjamin: maybe we should add this as a flag, as we do in SynthSR… > > Cheers, > > /E > > > > -- > > Juan Eugenio Iglesias > > http://secure-web.cisco.com/1IR1bx4iIiu483c-gubT-7sJz9-PHRZ1A5blSSl0RB6i-5Oq7Y6VBPrITJ8QUygst9SyCI4T1sIu_QuDmaBHNm5DuRZlMCX0aQHCv0fpUy-Xq4Jy9OD24jYHE-kgGEOvFDWKC8Yx1Zuy5xcuXv-rrVcbeNoSIj8CCrsv2_LqsKLr_V98ORWNt-IKEkjx6j4X6CEVlrOFW5SfiYdOoBU5tQtT1JKc4defdRrJ9PKjkohbxc5hj9LvTrfECL73uLC7ZEiWTP5kc_9x8w-6ruYnZ97LEWX-rjo4bphX2Dp-2cGYk4ifRN1M5yqz27YcONKg6/http%3A%2F%2Fwww.jeiglesias.com > <http://secure-web.cisco.com/1rajmSb1Z4X6hrVV7EC5tsUxk0uanEzSaSYaYxD1Egdh8AR6Hh56R4ftwHZ3VwShD-6P853CFDNvr-rulTBK7nI6zB590521zSlI2xndRFDCTdFQXWFZL71cI_nMoxCgFP2x-BPYJbfesBsX4B1BhoDD2zLwAc83S9NaHWxY8RXJEaAQooyHB7jyvHnWH5fSABbS_u5Nqs3Qji4RAvUerQ_3i9ndWjZDbjgWJtZrfaq3pdmNg-8NkfZsxg2-FXvLwnlOlA0BmnXCLqIPGpVLSD_9yxZ5510Lh7AGotI4m7DiXg2r_VRVsm9GY0qA9CTDIW7yIxkTUu8a-4i7mNB2UEA/http%3A%2F%2Fwww.jeiglesias.com> > > > > *From: *Gonzalo Rojas Costa > *Date: *Wednesday, March 8, 2023 at 12:04 > *To: *"freesurfer@nmr.mgh.harvard.edu" > *Cc: *"Iglesias Gonzalez, Juan E." > *Subject: *SynthSeg with CT images. > > > > *External Email - Use Caution* > > Hi: > > > >I tried SynthSeg using CT images, but I got very bad results... CT > images must have some specific characteristics? I tried with axial > acquisition and volumetric one > > > > Sincerely, > > > > > > Gonzalo Rojas Costa > > Department of Radiology > Clínica las Condes > Lo Fontecilla 441, Las Condes, Santiago, Chile. > Tel: 56-2-2105170 > Cel: 56-9-97771785 > > https://secure-web.cisco.com/1KzPea1YxgjqNRqHWvcKvdH1ho2b0l5JLB0r09f8HMdtZFBW-o6YLZW_ebBIU5m55jY5WtwD7HFOVx0xdU_J0_B7BCFJvGchSGjyR8TtCuFlbfk8msoDJwO1OuhIDUtBjTi1BFTP1MXlo4BvQ0eiLvInVHdfk8CmFl3CcMXW6Uzl6Gi0xm8NF8Iia_7nFhTJKSKHD8rPKd11q8TE8aGhOgOYYHPYdH_TNYZpOOcXt4QOhxVkrzEacEGmn1BQpvzDIIxz1Df9nxFXbtteDCq5HPkSGo_Sz2E3jDzIR4OTjGi7rTzC05PHyK2hGkNEmj_Yd/https%3A%2F%2Fscholar.google.com%2Fcitations%3Fuser%3DLO7LZ3oJ > <https://secure-web.cisco.com/1X4JTWBblTD8tld8oBtoX_hRATMKAHXt1kz8xQ7YPlXYPCFqdXfA0H2JSQd7Sf9iABw7ZXWREb6ZPRpqIjLu5kUVANuSPsw4E1FQrq8EcNcxVJLcJP8_61lsQFWfJtoEXAXr8kACcKq_PDEnngdLDzo-x-Napt2ob06RC1xuPwm1RwJWaPMun-E7X8rrcjsD6xf4UupYvJDfj8OSi7Cvnpey6_7zNIF4GBjHNUOcHEG-Ie9_RuFiTgQfOuTTQi1XDQmJ06W2r5MDwitXqElbSh7QTBTa6CxuYVhc03x81FuP1eS1BiUMk4yxWVGvd2JnzDm38adwdkUrQ4Esm7Ojhsw/https%3A%2F%2Fscholar.google.com%2Fcitations%3Fuser%3DLO7LZ3oJ> > https://secure-web.cisco.com/15WUSvOlDCd8gZLVKogIZYlhmV9KT_lzIEGdy9rBrhDdMkeA0EjjIq_oojTdHGd5pLmZIcF0sx3ksMtY848PHNT3zxF
Re: [Freesurfer] SynthSeg with CT images.
External Email - Use Caution Hi Benjamin: I tested with the clipping, and it works ok with a CT image. Sincerely Gonzalo Rojas Costa El mié, 8 de mar de 2023, 14:39, Benjamin Billot escribió: > Yes, agreed. > > Gonzalo: Also, if SynthSeg still gives you a bad result after clipping, > you might want to check that the image header is not corrupted. > > Best > > Benjamin > -- > *From:* Iglesias Gonzalez, Juan E. > *Sent:* 08 March 2023 12:25 > *To:* Gonzalo Rojas Costa; freesurfer@nmr.mgh.harvard.edu > *Cc:* Benjamin Billot > *Subject:* Re: SynthSeg with CT images. > > > Dear Gonzalo, > > Can you please try clipping the input to Hounsfield between 0 and 80? That > should do the trick. If you have trouble with this, feel free to send me > scan so I can take a look. > > Benjamin: maybe we should add this as a flag, as we do in SynthSR… > > Cheers, > > /E > > > > -- > > Juan Eugenio Iglesias > > http://secure-web.cisco.com/1oY_Ta7QUv3TybD8UgzuVG9Dc0uElb0r5sAAb2tL8RYcVO1ad1RZJfZPIrjEo6XO3v9O87WCfbACLlPabg6MB3o3JWN1ltmZzhc5XOzhtnEfzE0VGCM3drJmNP7SzceCkqlvjYXVetsAHj-k8cw6SLEwd5XlnpPjhtnrE4mEBu0E6-Q9jhYYyMf9_YnmfwnTbuNqJwDSLhA5XLroRcyZLHVqsEnrI1AcevgHk8m5m4A_-hxHovL5R0tmMkog5sZAGH7vMawArRXhN5kaGzBX-ub8yHgjY7jVFczyhKtzO6F_uGy5HEci-MH4bhM4m-4Xq/http%3A%2F%2Fwww.jeiglesias.com > > > > *From: *Gonzalo Rojas Costa > *Date: *Wednesday, March 8, 2023 at 12:04 > *To: *"freesurfer@nmr.mgh.harvard.edu" > *Cc: *"Iglesias Gonzalez, Juan E." > *Subject: *SynthSeg with CT images. > > > > *External Email - Use Caution* > > Hi: > > > >I tried SynthSeg using CT images, but I got very bad results... CT > images must have some specific characteristics? I tried with axial > acquisition and volumetric one > > > > Sincerely, > > > > > > Gonzalo Rojas Costa > > Department of Radiology > Clínica las Condes > Lo Fontecilla 441, Las Condes, Santiago, Chile. > Tel: 56-2-2105170 > Cel: 56-9-97771785 > > https://secure-web.cisco.com/1dx-ON0IVqdFsAlkwbnFP-5CWyzUsWOqcXmV2sh2KowfhnOPME32OTUSeEIxP0nZZHuxGlqiOa0yyM1EDsnjjGyhKQeOjfeL70TeYyFH9thOaym_uT9LbfWIoXZAlwRSeUCNuYiIW89EZoeXD-Gt4kNfFTEznkWgcwzAhVxdxGAtfmRoak5NoxK5wOzdOrGmr7GT8HFXir-Fu9aHzVLXUql-nEuO7ZHH_SyETSIR_8HZZIIaDI7kMV02TYgGVhMFFBXW4MkoK8956DcaRJRn8SZswrVzjSS9OAxlX7FSwBpiO0rXhm5F92uactc8TRiak/https%3A%2F%2Fscholar.google.com%2Fcitations%3Fuser%3DLO7LZ3oJ > <https://secure-web.cisco.com/1X4JTWBblTD8tld8oBtoX_hRATMKAHXt1kz8xQ7YPlXYPCFqdXfA0H2JSQd7Sf9iABw7ZXWREb6ZPRpqIjLu5kUVANuSPsw4E1FQrq8EcNcxVJLcJP8_61lsQFWfJtoEXAXr8kACcKq_PDEnngdLDzo-x-Napt2ob06RC1xuPwm1RwJWaPMun-E7X8rrcjsD6xf4UupYvJDfj8OSi7Cvnpey6_7zNIF4GBjHNUOcHEG-Ie9_RuFiTgQfOuTTQi1XDQmJ06W2r5MDwitXqElbSh7QTBTa6CxuYVhc03x81FuP1eS1BiUMk4yxWVGvd2JnzDm38adwdkUrQ4Esm7Ojhsw/https%3A%2F%2Fscholar.google.com%2Fcitations%3Fuser%3DLO7LZ3oJ> > https://secure-web.cisco.com/1WfM5q5JiWue1joAWuZpJ-2gnXIfCTH4jF5i5mncbvG8VTbpepiWrZke6WmmZMgAgoKJE29TQDYVXrLaFAIATApuZkVxgDWHQcJ_2CR90AMpcKuMCTBPzze_8k34CuApkK71BRD5lKroK1GzyeaDtrGErzMXaH7qKgvUdJgv1MKrApnitPytnvSqRY_rLBHZYusFRl63drgxq9THhMAODbPy_ssC-NfB-xCjb-4WRuMNEsnCy7NNRke5cYl3C_9pcO19L7NBw4y4EzCBU7iVHNFd6WPrhNGSJdx57dMbbqmcPt-WmfOdiOkMX5y3j5SjI/https%3A%2F%2Fwww.researchgate.net%2Fprofile%2FGonzalo_Rojas2 > <https://secure-web.cisco.com/1jIR1VD1EGr6FdxqTGgScWCn_mHW5DPrMZAjfRggLiGtOamcGRinZiM0HNnQE0ybVKUqF9WJYOq9a4QJzt0qFHoBw_eIv85hrkDL1pJNd7WrTFbj1RjcPFatMfv-bsxG8I7zoXYh2maIFCWC4iz5ELXiKCr1WTkvsIeZXu5mQCEkJ3eB4sCbN5x-CT5YEOaxPEJdOQ_t3mNDKTN5ORe8om-TzD7U8VDs-P68_-68BvQm3f7CDK_xEW4nPWvaGT7Icx1cqkRXMZKWzs340o4vkCM4EJJ-o0J_RuNGaGs91o5BtOKE6AE0cFdL_6s2NTOKhD2uLQp3ofHyAuuQKkr72vw/https%3A%2F%2Fwww.researchgate.net%2Fprofile%2FGonzalo_Rojas2> > > https://secure-web.cisco.com/18CztnN9siLRgJ0-UmgEchKrQq1yBr_pJu3oqRmA8vMLAAx2KUpX8WKcfOvUur0y9Cykrj6i_a3f4nFXwFGMrUdL5HUYiFNgMjTjD2FAuuUY133eg55PS_fcek1FvV11BdXxiAYyhlZeO-kSLZ6czfh_fO1dPiXMnmJ2LS2N-zG11eMGTKTBNMWfCX6qeTo30yIKbC6eJfMkUrbZbOpCpuDcTnO1RbBhuVnJCgaLE89Ydqwk8etX6d-IPgUvLnW0Sx5-Etq5z28SKb0Rr8rvnW5HkNFg7sQBUjxQqfttBm1xe8vg9_KnuSnJvlJGF2Ld9/https%3A%2F%2Fcvn.fecyt.es%2F-0002-6228-2678 > <https://secure-web.cisco.com/1yA9l7ISJLI6AsyMtjg6tqVLF4b_n1UlUVhia2mXbDUAX5fGZyZcRqNTfuohp8mAbc_ACa3hgSPYntMqG1-0fDtSgts2OmLxz4QnX6ZHQZKM5PyA7BrbGBzONTFUBMDYgc9zYNZbdJe4xL_hLWAo2R4UEFgI5rD87fHAWQabgaZwrGmQo79CFJvlemPIiBO2e7KxArWWjicG-y_ekICfjdeLuFvdQ-w0tXfXupw3t0jYHJ_XemfYZZSYZnP0Q_2UclHE7ZpsQ_uAGCpXBiR2TmPLXbCn5PG0hA4Drp3aBhP-kW9P-NRZeMBjGO6M-grFIu4fwZrTuuKF6wHpDWR0qWQ/https%3A%2F%2Fcvn.fecyt.es%2F-0002-6228-2678> > http://secure-web.cisco.com/1wJM_skjI0l0zygtqAs442I6qKn4WaYZxNrNXu6J9to22-8I_uX739EMQ8WtN6BEtH_X3t3XEZW2i1FSs9a7HE7zVf2BEPKeU-cnTa1HzYLT-P8gGIagYukTq7s1G68P
[Freesurfer] SynthSeg with CT images.
External Email - Use Caution Hi: I tried SynthSeg using CT images, but I got very bad results... CT images must have some specific characteristics? I tried with axial acquisition and volumetric one Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 https://secure-web.cisco.com/124lTzPUFk2g93tIiOP_RZIKtO7aB_xIAzR3n-NFnpRUBDC5dwqaF2mDGPEnkEhr828-40cnX6OmR2H8vKVDdgQt59NViEyx5q5UvH78bVrQQXWHpmCQcPafwTybP5QvG92L14wQIfZAm8NJFltRp5ArSLEdVhxBKyE0RIk_4GPursWu6BXRuPbF9OAIsLXEzZICPbEp6ODOc_VFbbDm81FG3uuUho1PSKotU7pNEJLoEoSx05HzUDo2I8H8LumpEARTTW8PrpE6Q94Wq4WkNOOoPoPC9_Q9BEBjjo5BV77KPylvPaVHCK-tcLOIXGxBCEibjQZ479Hce7P--aYX0Cg/https%3A%2F%2Fscholar.google.com%2Fcitations%3Fuser%3DLO7LZ3oJ https://secure-web.cisco.com/1j0ISp47eIFtrb1e8T61MHEGaGOjjkY7X7EP3tl6QI9uUyVq2pAzs0QGka496H65p3DvWp5Bcu5orTPlOf43inO3FCn6Lq-KV8oK8JLGtgL097JmOapknyLkhzHuPEt7PCWKjbtz5k_-AZhmG1pLdRtki0H1yNym61fe55J9dTMaF2av4limkBu6wW25_NWr9RvZ3j9LntQRTwpPGM8qtqPjuQ8lSpYGlTRSC2KTB83Iff78lshJ9-7xWn6i9m5WwMD7kpMZDzZ4NpMN9GBj1HiUjRzXJQQR38Eb405CsQlYcyKOH-O_WkRYZoq8WWEW9z070Sri7szgLVCzA324tjg/https%3A%2F%2Fwww.researchgate.net%2Fprofile%2FGonzalo_Rojas2 https://secure-web.cisco.com/1Y56xwcQwRV4t77xO4h4FW-bL40P_UtP-sWKcOdTY6xL_bFzx8ihJ_9Tvs6NgHrvnsBNg7qw5L6B_Qv6jtsSqGbBQm7_HuGTz3hXTOvO5Br11AGy_3adIP8xyioEGqUgQTaBfAAaKLKqaphDkzzX2M7Xyr_jX0rEZEmALOqjdz8N6Z4E_fHE55BMMv38gCsWy4_9Ak800-bG7KcHHMx-nrfZ50b6MG9D6uiKOqTYCQzDRhstpnXPjeVjMNgjhBpLW_pWxDzkIDa71AMfZ8jvs9tkEPDrsbv6DVzdPyALllS61TuTEgmbV5IHU3tctj96PgKLWxmBHnLgMWRLE1oNzGw/https%3A%2F%2Fcvn.fecyt.es%2F-0002-6228-2678 http://secure-web.cisco.com/1jDmtFL__LFuOoeWvIVy_NxznOAMBVzwNnvweeEquHeNDvBHMQS7bZz75oUGkAHEIprWxBCrHzP0omOaymYCd208nC86l9SVSX-qvJ_6SWnaE5e1ovpA8-exHINGfeHSIvqqn2BbxnpslwuUqo2vnzelqcpKRkI9YZFna85XmDDh4lalTafugQNLtZFKLLSeTvzY3gll0syMljHb_qkJRdUv6xoRAB8TCx-Dr8HlbGBBa4dxV8s7w6-vPEDi-OK5GvjdjiH3QxXkRceFgQfbmLjCT-SZQKehC-BE32TqunxiV_jgZX5BCko3jPrx6ZcWoGdLJ9sDlr9YmL8POnTg9ZA/http%3A%2F%2Fwww.researcherid.com%2Frid%2FB-2036-2013 https://secure-web.cisco.com/1zOogV6Olu-Gbu6J9GAYf7iYCLr5rTveKf3HrLVn5jSdNRTYqstJDcpBbW7M_QsqGBVdpE6f8JFO-zjrh-WGsSeXxpr1hhQClcq6pYlrCMeW9RPIJURTZ_1su0gkXBNo0abEvVfQwHWzSZ4DbWlqSaMs52CNSR1OML3UlgtQfY6qz_3ZnYkK-3ILPk6FteR-VUgCVtY_f3qpvBSU7446_diGZ-yNwOeEp1oMA0saIQKvTHxdNs4gDRUep_N3HhlWtxNozmKF4BB0vc-PcdmlBw4CiBiByXGwWgr8baWKR7HkIZhpygNAfNV_NhPJ5InxTZdJbwB4karMuDNlnGEmSPg/https%3A%2F%2Fcl.linkedin.com%2Fin%2Fgonzalorojascosta ___ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] CT conversion from DICOM to MGZ
External Email - Use Caution Hi: I am trying to convert CT images from DICOM to MGZ using mri_convert. When running it shows the message "INFO: applying rescale intercept and slope based on (0028,1052) (0028,1053). If you do not want this, then set FS_RESCALE_DICOM to 0 and rerun." Where can I find the FS_RESCALE_DICOM option ? Sincerely, Gonzalo Rojas Costa ___ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] installation of two versions of freesurfer on same computer...
External Email - Use Caution Hi: How can I install two different versions of freesurfer on the same computer? Sincerely, Gonzalo Rojas Costa ___ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] trac-all error
External Email - Use Caution Hi: I tried to use trac-all using following syntax: trac-all -prep -s name -i SIEMENS_DICOM_256_GRADIENTS_TRACTOGRAPHY_FILES_PATH and I got the following error message: "ERROR: for B0 distortion correction with reverse-polarity DWIs ERROR: or for model-based eddy-current distortion correction, ERROR: must specify PE direction" Why? Sincerely, Gonzalo Rojas Costa ___ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] infantFS computer requierements
External Email - Use Caution Hi: In https://secure-web.cisco.com/1SdvOIph2KSxWpJgy_wKxKUUCcAtbANooEGXP9aUvNocF250CMSnfCpY67ED46Co0c91HTyR4fyniivVIVyf_jj5R5vx2SZFxB2RVQhKeqrsnHXcyyptTF2fApVhY-nsE78OjrODMeKEIBvDozWzGjHbHbB_bWoHchPoU0YJ-Whe-9yBq8Yw6G7wuNqgwpK6N-ij6-vh6vytQuKJ4Ac7eZth7u7hbHdB-oGnxzMHNe7NgGgPQdoWlja5jBByF9X68VwYyO-624S57RKnKddm5DrYUqBqXu0bToLI--mxRwxESvPvlNmwQRERSuggE_xI2K6buks59pjkHljuWytWD3w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FinfantFS appears that infantFS needs 23GB RAM. What are the minimum computer requirements for infantFS? CPU? GPU? VRAM? Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 ___ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] T1 gadolinium
External Email - Use Caution Hi: SynthSeg is useful for T1-GD volumetric images? Another algorithm, software? Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 https://secure-web.cisco.com/1I2XJrWdFnZxY-dYDbiZg0PV2H4bghSVXCQk63X1VSya6anSyQJv9AE2DmTqKCS_pGJ1rUzn4EKDBsMxGgxi36aU2ol9AG249ANjc-p0gshefU7IDmOWAf0BEmRpO3LG0aGtmgl5UgPE72CDm-9wFufEswwNPNCXfh1uQ236aI6nHXouVHALw32Hp3uTEHQ3epmsT3wIvNKKG2sgP0WAzYK8k7rU41-z-2aNAuANjVkUQgYO9_rOpkYYw7k6OVQtZU42sciDAzDpsVW9iIDKo2p6GecQdDYuiXNsmyUDwNTId99I2LKr6hAC6K_42OkOKcoLbSmFp1-N9gRJeKkMuVw/https%3A%2F%2Fscholar.google.com%2Fcitations%3Fuser%3DLO7LZ3oJ https://secure-web.cisco.com/13zfZJFRpU2hG9Abh2YAV0LPmd1V6ff2BdGkKw7NLlRJY9LOtYd8wwEoxlvD9G7cyGHlvuFyGFWoO9GCbOCw74KnMe081B7zCpzY5yvRwanCuQ6pin51JfbCrmFDrZotf0HaF39vO53RWaKeuFjA74jFwHqZX8AKI_4chzf4IxkLj56xLdQdaH4ADx9OCzgVtSTzlZbm98Kvzk-IzWLlSa_hxKUqALyDHWXzFSlLIxPKekRkvPITm6G51x7V008mgSIhfcLus9d1SHxkL3zvLLNtrrZ8IiRLqH1q1sMFFtprFu2hqs85nbsRNlO4MD02O2YfkdZkG6qj7BoZ1WTqEkw/https%3A%2F%2Fwww.researchgate.net%2Fprofile%2FGonzalo_Rojas2 https://secure-web.cisco.com/1p2HQdyHZcPFsEa80XIMcd_JLnEOosZMvxjlvKnim0-NVWjm7KTCFp8zF_RfjkJObZ6mxcabl4PxFjcOrFsWPoQYQyyrQ-zkCQFv5soZhoXHa-E5unkQn-3BrZLfa8T48RPBDybUTXZRE1sgwLTCnyMCKNq5ZyfQzyWq3w35eXnhQyfaHRPG5s5U5i0fFQU0hq5_zTIKywm6U3g3H2Z38DVSIlsyCfN_zvapcXQycK8OTgAMtW2NcvkyutSc_1v3LZwzx7vR7E8QCCZ5HUAk_xxh_C59D0GKR2qVEOFQLk0T3HEmJUJnJbBE7f0ybeUjbGsyfexNTHLRVy2jf-f-csg/https%3A%2F%2Fcvn.fecyt.es%2F-0002-6228-2678 http://secure-web.cisco.com/1t-sL6HvQklTyxVFyP8KzIDoaaMPtJscszD92RHMNQuJE8ku6HIpY-h5l2hr9S9awb1T8EiMkPgxyJFl2o_hoxmElXXhicVsFgcBZW6-F6EsxMAtym2rhsHMRvWx4DMMIWBerjYHe37-_UjeEG7feJBsXojfp6-kjcy9TiB4vUqb2McxOIeK4wBFqXhibqaaPLizMAy00dmZNhQDJXOJ25cr3p9FEyoT1JbcpmgTEnWlL4IjjSLgR7DnXaaNyybbcA_4BRKdOztnGxGMo081VZrDYQbk9cdc-S1rgfoqs-7FWs9ATEP3VivZsLo3UYNAzUJtxlh7LbGygb9ayueEeVg/http%3A%2F%2Fwww.researcherid.com%2Frid%2FB-2036-2013 https://secure-web.cisco.com/1DKuT3Zodsn-rxAY5cLCK0zkUQtPg9820KtzYLjm_ymXLaKtPV9nTFIADkKpBId07iJQKvvGO6K3_rEo1hfgioHVEEs0MtAVvNK4tH8IKbu45aGQbVG8JIQYFiUZUynUHnb51A0pzt2h4MIh521EFc3FsBtVoy3RXLQh4sN8SjOtEGfHiGVx3wXZmCl0D46HbioEHxXmfHXgarc9kKaz2JowHJhj4Pcs_IDRf4hfSuIND_8cOUs0LM1VW3uRcUIvp7T6XSMTG7q2One0IKPV5r0XekGmtm9PeJQ1NTi2bwMly86UW4E09-6RofhGKzdMjxLQnCdMx_ihJyGDMmuUeSA/https%3A%2F%2Fcl.linkedin.com%2Fin%2Fgonzalorojascosta ___ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] convert .reg.lta linear transform to an ITK transform for 3DSlicer
External Email - Use Caution Hi: How can I convert a .reg.lta linear transform to an ITK transform for 3DSlicer? Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 https://secure-web.cisco.com/13TZ07AstA_Q_lsIF4aiCFiJWD-gpdMOlT0cLc-2oTVqOHAg5qg645Pg0mWiar5CSOJ4X6gEhAiwSXX6fjLT59l1lwN-atxNKzIjViv1vb0CSI7gnyAA-afnwkX8Cx9plLxB-VbnJU9ULlmRtxLBjlCeQkye8357PrmeSQA3rkXldeenp8yfGHmqZ5i43L2cRxFEAOtyI0q2EDppwIvIKDx_5GIutv1XWC2M_vwXyaUYhDx6rka5VyrAhrpGCEg5bSmUKmfww7HCvE07uQpo6TmE3tsYmK3n8DzzWYvPRaXLGahVX6acm27ZP_1Jx4ox1VENyeF3i3YeszAlYHI8EGw/https%3A%2F%2Fscholar.google.com%2Fcitations%3Fuser%3DLO7LZ3oJ https://secure-web.cisco.com/16gO9CNWzQHT7IqdPqjexT9AfEDEQl7WrLvpp3Nc_AtMNweH7yogrcQwxR6MJnzwH5X7YumZfI0sAefmgeexNiHd4hvkC5OKtUkLzvluTG-oXq3pw79FAdj7rgolimf0-BY_wtnW0UxfSZmBGYsQ6upSeHZm1vNorUH-LUjKIpUKI04UMLWvbUMNAt6e6NN9WA_Oo1WU6U0msCbZBTkDthRYQaTuFGnPWMhruTDw7sSyHqlqxtFlBjoHOUAqS_ioWIiXwrZTsJTZZJLP3ksj0KABBowGBYj8a6A6xv_QJyrejtfrSadsjQg6XCCg4x6TxcsSDu2tuv_h3qPkpukX0pQ/https%3A%2F%2Fwww.researchgate.net%2Fprofile%2FGonzalo_Rojas2 https://secure-web.cisco.com/1gyom5cJyQ8cmW1-ISZiem0NN2me1FWbxC3aS-L8jw2c7mahWbba6QVzyOn1LZvZUMI51hPwWH2czS0i69t1VNI7LPfjK18GMMY56fho8iubQ4k4nXBZLuzDrYK7RalDzWc2lAa4NbWpJBFiptCzbWZRV54NdaRKzhRneECZ6kM2PS19OGWh7ioIZ5TGGsx4BueyBdJqV93XkEtX6WseF-ujSkwcicVRzyDBL6Y1Ia3DISVNAwaSF8d8Y5nBS2iJR7upUDRs3MRZPpmRgiLP35tiWv8bpYTnlryBY8Br4dE2UUzJ9vf_y1msKEA8S-TNAjiPgG5hfqpJoP1w9IOMYsQ/https%3A%2F%2Fcvn.fecyt.es%2F-0002-6228-2678 http://secure-web.cisco.com/11hSSrxQ5y9JDhtiyawoQm5uEXQUx4ke5TYmqszpC-smAH4jXoGSXunbDrzAI5tV_XnQVxoRXyGuRbpoMcYLE602ySdTo5xupLyJ9x9B0AmKQ9IKHnu3nXUIiZdZo10jWq-yjNMfybIB0DRTub1gF0UUB9i9jNmRTphzDgBilQzjiQfuVMGVyFKCb8oWEh5X6dhRfu4AXRjHbaIMlgxY3N2NSeaYhpBwt-TBd4LbKfpYbK3_8GK20o82AmyMCVIm0sUgwFeiqLsE5OVRgCqbd-M46OKscyYwF9VQRn7BCqdo7uQl9M7SjmLBBcs28BOV0RaoFTIQXvHkI9x8zlfKdgQ/http%3A%2F%2Fwww.researcherid.com%2Frid%2FB-2036-2013 https://secure-web.cisco.com/1VUiRWuUGVZcEiJxtLi98il3aVo2D9T3cokDDEuMEzwftNIYJKYsD0r7DlAxTc5ZF3CmcqxOX0dliZXFFy9F-EaWdNdE-0ZswT0Xb78clzl_d9_rOIk-6bzplZV-rb9lywVUPC-G_X3_DnZZkI5gyHLk7CNBQBO050Mb7xSaLZGQ4hoU0MOUTHV8OzyBGXOn3--_87REA7jJ-C9MhUUIlF191D3SmcTu5u6xAixdrvKz3UjbVEN12yk6yuKC7lkd5GOkpkad7D69vJsuFpXOW05x_TX2oup7aZr326HYDSVn-GxFtJ1VoUM4nKpGwZ1g-G4vsD36MIi9v686LIvLTzg/https%3A%2F%2Fcl.linkedin.com%2Fin%2Fgonzalorojascosta ___ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] load PET.reg.lta freesurfer corregistration file in 3D slicer 4.11
External Email - Use Caution Hi: I coregistered a PET file to a freesurfer data using mri_coreg command. I imported the freesurfer-generated data to 3D Slicer. How can I import the PET.reg.lta file in 3D Slicer? Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 https://secure-web.cisco.com/1e17f0KeEx1uku6w91Y5lIGB5srmBKu9TQ3WRtpCV4CmGcPmc5IJBaFlf7SCxC5gkfgc6X1L8HhWNvYNdp8r6c141fZCubYFiz2h3OrCt2SiKUSMDNXlMJkUYQO6cXXRiSg6AIVoAZ7e17cDE8pljj_J0FF_BprFekpvJXP22EfTbdnibu0Pps_vvqaMI1hH2O78fSgzxoEX7UaNV6ZQtIg58Vmt-a7jewP0OCV7K16BR1OFxqcJTXl0209CHtlyA0fqOxIhNrxjLEQuAewTHv5U_jWnvOGumegUWnCAdGIQ_47GoQwsTKGkszjZNEkr69sdV5WDoP1yTuR3MAdvPrQ/https%3A%2F%2Fscholar.google.com%2Fcitations%3Fuser%3DLO7LZ3oJ https://secure-web.cisco.com/1cs2LDGSTCr6GnV5Rq-K7aFHHjdJcgniT_IPajEDX9qitbO6etPJae5qbA8fiAdq7JwLXNtg0DvmV-2_kGiwEzGZNUORohki04Wh1JmsVTLXWc3r9wi-FLT4bxs7Ai-QrDKWjqHBTSueuC7cJCTTlS6NHP_DElP2mNTZLwJKalWfw_x3HYa0uRC8itRPZuD-bRnv6jT8t8VqRhAHUTUmdJ0PRdhsVSVTduxVPGEEOfBQh2O9SuEocI4eoGsp7Ojv6_8OMEfqKnbxcmSZMyL8HgVi-g7K9vO8pz-NW8Ts5U0pt_CDdinfVvS3mzhp-VllluP0QnWzOTY9GadcF272JNQ/https%3A%2F%2Fwww.researchgate.net%2Fprofile%2FGonzalo_Rojas2 https://secure-web.cisco.com/1c3Ub-NigVjcMlUsRtymIbNmw_2reyZp6e5kdQWcxIjWpRDtw6V5u2KLwfzXqZTiWGJFfd6vrbyp9SM3H2XHhcWKXN5jiZYqNilM9hnY3RlAyJ2aqmLlXKDr4fLlDvz1qnDOCfde9IOBkStEdflXJ6mUcZKATSMPoLYTUqewNspzVQDoPOWZHhBnz5GCwrTOAnhec14duJLQDi3WuvyOvHa2tG6xJa5XmBgQDBOPCLeX6GuZQlKjii8Lg3ShpZaP9qNYF961o4uCp0Sm0oAtLiGhH5pj6DpwrUxp7-ImIhHNK012A-hWH8y2XAuWIcEZGQA9Uy1t_4mX8InJthW0TUA/https%3A%2F%2Fcvn.fecyt.es%2F-0002-6228-2678 http://secure-web.cisco.com/1ptxxoRnoGXKniE15hzEh72mpWXmTkdcqzTdZL3sLc-LQjZE3NuXtAI2v1nO64F9-c0Dhxkq2O7pyyNkYRstAbecc7iQN_TkWK6LU9_fLZBY3oyDZ6myMhVd53STd9S0lWvcBJTKfq5aPudzQxlbvRPnnWvF504xFzJCVEIcGhTXs6YRUe3jSStsx5lttC6Rrhltz4-3RMyD83wQfuzKptYJXArkujI6nUvZto2K2AxiK4Ck_bzB9USoilW93Dru3MNUBihluyupFfj-ZpBSouKmARkFfX-ijH9_N2G9kAqgl-OKxs9f-YD-udl0OsxmXJWfVAKRz4OOqXHgcH5E0eA/http%3A%2F%2Fwww.researcherid.com%2Frid%2FB-2036-2013 https://secure-web.cisco.com/1V3s1u1ecjyempv27N_dkVM0NX2R9IvzTwxF-bXTbBaHXDJaH_-t_BO2pCP5qVmCgV9T-lGJjLjiey9UHUs0OtR1_Dou9zYLazQCrrhgdcQ6uyf_nkrUf1djajOzdwaIQUnUb7eMq3f_D6JzcNyarGrMi_k6Qxikeq-YlLR1-wsFu_Q3z7p1BsT33MnQBYSM5lnU79kCAp9t1-MegmlI56aTyc5sVt0wN5EebWdxjiS1ihzS8ZzbETN2nioox7U-vPrhxScQOIVmEZ0ghVW-FvS3OOIKh6Hs3tv6UGPprrEDQ_JoIsJdWoRRHMvliAvmdCkO7NYj7DPr7fe5y3HQPOw/https%3A%2F%2Fcl.linkedin.com%2Fin%2Fgonzalorojascosta ___ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] TRACULA question
External Email - Use Caution Hi: Is it possible to use input diffusion files in MOSAIC IMA Siemens file format directly? Or is it necessary to convert to nifti file format first? Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 https://secure-web.cisco.com/13PUT3U3zuLu0QBvcZiGdm18njGuoQr6dUsSQj9e5H3gOiFfFDIQfzquemma2IXSELZNdhFwGi3w3goGxGPnOUdDoh9pHJjjlEzyWgHhOvtSI1rWfiptKHRGKPqroO3HfU5LOzYece7gEBewcRdacnxbyoGkrInzayFlpCHDwMovVj2RsZXoAPA1TJD0c6qPpjpyNdRSfvWEQjlWFseO0XmY2GzERvEGLNZ2jVD7cFivFtsBZI6QKXubnoVYv7ZIhYdk8IDuEDnUGkM6aGN0fQdo0EfKqqQ5mvrA_-URQ1HAlx7fGFKcWaS-msf5JV3UYewMKh29ySoudmFsGrqP2Jg/https%3A%2F%2Fscholar.google.com%2Fcitations%3Fuser%3DLO7LZ3oJ https://secure-web.cisco.com/1TdZ-Zm0eaCvN4RyCzzXuq6HNPTVfbbxwGyNTIGMGFiRfybDhlZfcJej5DuQlBFxYwDJwSO1NbZisBp1yVrq7nyw2kMBF6oos5kUwQY5n5PaU_F0e5FlhFPXN8jHJ9-2ZjvCR48B8WX_Z98dUDwJgPDp6W5J9Qx86YoNJpPWxzK2nlRZBUv4m4xJZ1yZl8bc-y_rLC_yBmefTddoYvHRgxm-Sx-sI3urGbmLlgo1GW0ejAy5O87MgIVb9l10EMEi9Scz6WXE-mZCKUDK68bg0_py0KqpFw23M8fQvUlt-KsNQxJKwM0xjpEwDF8JFFDEW1fwAuuxSsUuDnVYZUTIW-g/https%3A%2F%2Fwww.researchgate.net%2Fprofile%2FGonzalo_Rojas2 https://secure-web.cisco.com/1lJu3jBI0nOfv9_IwBeCbcBNGA2K6pj5tSumDqMfk3ZItRd8BPyGam7Jzi5vwYgKSWZn_h3NHNpB-2LvnR0NG2dicPxcNLIMT9-kyIhxlIVn9KJDnI0UkMvvB_bwD35c9Wo8ZgYrmeeME-Xhopc25SP0b4uZ_ac8eyRU7siPGYplCIdV_wlbcpaf4QKngZ0GQ0OlKTSFA0kUvGppEUPh0dKLd1GGfVI7ta1xtDWAEeQDRZIJPDNENvLEMET8cajKIPIxhR0Pj9mFACW91chNeZqqgUH-RWTQD6lH1n-FqHFhQVN7buFLIgM89GsJppvGFD4sZGKjuTmnCpl4rS9rfaw/https%3A%2F%2Fcvn.fecyt.es%2F-0002-6228-2678 http://secure-web.cisco.com/1vs-E3PvUdSdie9Xm5LpQNiLpowx1KB-bnADkKZ76Vp4VANi--BPTBe90wM8SCdFK734_gIbmMr3PBFV4ZJOOJBA24RG16y2k3uomDr6zt-G7miVY8bETh1mVxRJXumLpmc3Yy3dH2PFE6uhzJNvuE5hUZqhTfQw-X7c4anBMhN_zYMez258yi_VwfB2Bz28yNTA0qClOp844_ELq3fX0tWSuBqUJmcCh8gyVYmA64LHU5lnFXwPdUjWzaoH9ZZ273niweURIdtncHPz5NN3wKifGl9r1dIbi8P9MG0Z64fjTArReR1NbSk-Z64E3_nvqJ-7Si7om181qm26Y05GJJQ/http%3A%2F%2Fwww.researcherid.com%2Frid%2FB-2036-2013 https://secure-web.cisco.com/1FM_I0dgNRRtoYqJmIXPdHgx__9woRyRSo5bnLSxgt51fCtFxOKP6SAvGDvzMdI6MlI8dr1A-GDLm7Ugbz4xQx_eBa-r6rF_KXZvcjQcG7c3HVqDBJ5Osza-xTwzP_JY8XT3vlujEpbz8lruWJRubpiv8DahDeUMtd6pNWEUHJagvmUDsyMHXbd1pm-XmpTmfa1RXkgkyaVwFfLwauPMJh4WFhchF7wz1ikJ8evtbLmu13H0jH_fCDLhFjkQlIHGSX4u1iiBtVtWcQQBc3tYacYBQNS-ly18qBzxa6Ebq21iyHPLMQ5lsZwvlRZoZl9d53xxdrTkwCPcwwkvO1szKIQ/https%3A%2F%2Fcl.linkedin.com%2Fin%2Fgonzalorojascosta ___ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] "B0 distortion correction with reverse-polarity DWIs"
External Email - Use Caution Hi: I tried to process a tractography with TRACULA. I got the error "ERROR: for B0 distortion correction with reverse-polarity DWIs. ERROR: or for model-based eddy-current distortion correction, ERROR: must specify PE direction". What does it mean? I read the webpage https://secure-web.cisco.com/1guG1MnfZf84DwQHfWaHHLuw6SMY7Z-tutMOyUkvQB8sNK-S-CoJR8hIxNUlraYAt1Q3nZwGPAObEFIpajbWVzXko7vE6ouZP6d3cQer8LgTmlBNzQzSLY8DEk7cj0Ma3noqeXSnVZBMcGgMyCGFELAc-ReX5c6q891gCUl35SRXIWZUO0yvLGMBLAKZQpvywUwHckAUlf5_8SQ9ch05XQW5ockkLH0E_yaqNOGE5DPhCDJRX5qjywx1yF5JcMkcPbiNNbEc34hoNaOpP1Y0xmpNNirDZiIGlgBoFYRkmonGJsbGHxJHNnN8Vok295ZKv2AcDxmDMdvWQZIyAINNHpr5ixKNj5750wSN4LPTZHn8/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Ftrac-all, but It was not clear to me how to solve the problem. Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 http://secure-web.cisco.com/12GtciP9OUiW5DkspMfrRVy3WsQH7lo4AsKjg0Sj8uml6hmsd8KFZr1odJEiUr6HRGBN-SuY_R4C_Y0XGK__GjtX9PjfFlQs2JHPTJLzzQzzy4y96uBuIlvSq_e9wiESYdSoS5y3QsDzt3ze1250ehvNQffFL1RD081jdhgsX7nH8Gs6kzXKYmASbPRIgy7kPPm7w8j0tLkTM-uD40PHVwQjblo3F4ZND1hdrlSk5nitHr7H1v4C4iuaX6fP86dTzzad4WCwFYWqtxusQJ4IJ6YfGwCbquzJNQDqCxj9P7Z8d_jXwKukNBPPzPuyzoCPmWp5-rV1tyuGsoPIxR1yopg/http%3A%2F%2Fwww.aribrain.info https://secure-web.cisco.com/1MqLKS1F46RbplHUM6h_KNyjN0BiKcyL58vxd1gCfQMyaz0OPW17_nrs2VG9SJQNHeXH4IMAeEcl6px6_zaUrsPw6AMcQ9-DcUneAhxAncGITAtkY6jjXUmvoPFRcZbSvtJBZRHQ2syMM23Bxfv46n2Z9qjyKI69GXBt701RXajzTrug8rL4CL2MOY5dedYAfyrjlaSulR4uSa3gi9q8VzVtXB_ow5ZJzK441W9Nbk71z74J31Bgk8Qzk_qgFB4kOQzdozHIMoD49K52MzYR9UbK2rXbUETVeg49T71HG37OiPJ6SEpvLF3IMajM_tzSVR2eJxDCf5oCoPhagT5UzMXEMsibitSB6UryFporqPUE/https%3A%2F%2Fscholar.google.com%2Fcitations%3Fuser%3DLO7LZ3oJ https://secure-web.cisco.com/1VYyKt8bpinu3O6RicUYTbOJmllqjZD8fa4vMdxnypEQayQ9J02-zfQoV3CaEPXmYzY15Ptg-iiGztazIob_nLawvlh0vRbpslrQ9Vr3rIhHWe9I4lbE1tKCPiFgb3kqwSQCahbny-Ve23MayOPyzb1gscRMpyuAUi0JEJWrZCSM-Qta7stv3OP5XPvKEwKUmcqk2KFgiTvsX55erZbsnadmzuXWwYPhgHM5uwwNwwyQkfwe2MAhTHWy9Ow7U-w-EQO6iS41z2mTuTHg3oRu4ZAOrmYNLvENgXyRP94a_a2h3dWJuSiXp1efuxUDLNNTOSOeNv8qjVLy-wrExLZqhuQnbOpvYRV53-Tzus2GKzRQ/https%3A%2F%2Fwww.researchgate.net%2Fprofile%2FGonzalo_Rojas2 https://secure-web.cisco.com/1cDJNj5GQNOJNQJmRBcgfx71cRT_O6MgqP1ftnJlfUY5Nun_rWo6B88PBnd6lVH9efnoMI7MgyT3hCEUUToJuRRK4Ckuyc6VR4HpWGQNTKk2ejcknhkODOU2BBSo_nE6PPrryQIObssSSJ3xqzSHPlw54l42nLje35IFdP972Q8_zAIYcascWSOV2Gf4Cdl3PTK4B1cSVYW3iEGLQvh-23ZhfQzKV0NtqfzRxdTadhCQ6ciHt7O9MthJC_zTk7zKeaEtgdug3_lN3ZqcqFSLWDRgmDCCthA1Odtsn-uKXY7UBDFeoHwt_1xUPDBgAcurfDbXKD5Ai_55MCCOiYOZcVK8g8bon5VGI5ehCWH93GE8/https%3A%2F%2Fcvn.fecyt.es%2F-0002-6228-2678 http://secure-web.cisco.com/1FaAL_RhtLAORTKofMH0umP03Sz7z4fz1ix6_BxtTBFSkxZd5Ij8oIERZT-ntsCxShw25L9g_nXPFsw0tjYLRNsjpyxjvBoEpivewpSxRM-hBIkDyKD1oJ2YhK2qkbhg8h2O8p8RL89bq8Qg5fnXFsEcvn2nVQoJzszYU5x3qdg1G0creSaAwIQthPDC1mPmtYEJUQD5fDto9s7P17o-bGPfCipDCFNYvHnnH1Olo02dLBOCIMnLuYe0gKlUygt4QbxzGN01qZT24YX1HbozncxDFNEM5hcpAPzv885kr-ff1jGnzctH3rJn3evnhun_WZlm7pCcb2LCZLEhDnEUUzBI0ij7ydAXqXKoRaMTvJNk/http%3A%2F%2Fwww.researcherid.com%2Frid%2FB-2036-2013 https://secure-web.cisco.com/1Chz4Nd2Gs4bv5UU_W7XXxgXJhQCBYB_9QHiTrY3XemPxP0nrw9NRQ4rHSVW3l0pM2TlRG8qiviXBOXTuNG5PNC479AlRMDtEIguFfyxUwj83Kmzat3oXNcVnBeslRPolAY5uMw-BSFORuL70qD-W50LcdIaNkNQ_jbGIJqm1NkCWabnBqUyzcHY7KS-G6rTGXgEH-cwUOLmA6uaXmVzOoPcnir1R95kaqEh1kNLy-NsHrHoa0-KKU5VPdzCizrIcGnUeO_d7oi_FsVvUUdhU1p7TeqvjU5ML64yk2jF3U8mlWPxrEtM8Qdzk_nFxIltn6vfgCeEXYv5xPuIgF3u3P5Mcwo3jdPpOv13c7Bmcb-o/https%3A%2F%2Fcl.linkedin.com%2Fin%2Fgonzalorojascosta ___ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] “Illegal instruction (core dumped)” in mri_synthseg and mri_synthsr
External Email - Use Caution Hi: I tried to use mri_synthseg and mri_synthsr commands, but I got the error message "Illegal instruction (core dumped)". Any solution? I have the March 31st, 2022 version. Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 https://secure-web.cisco.com/1A3UQ11G-wOv-3pW2zSaWtZKG8SS328lgaqQXucSvEjh6odB-KDmWxYXm4OCFP3VTPEYF9hixnewYKSlG7U33uk7GWkTJW6hJiGRkhdV_vDr7AMoQ_fDtCehpAMSERscngsF_9sVywi05i9ZSVyFj92rhbO080hMC0i6fHZ_MZg69OILUh5UpP4_dEkx1qnSe2RZRG9FibNQxe9UsmqWHfXxwUZplkELriSfTXkcGJJBKRE0sIKnqxcf9cJaaCAIILk8QvhuDqeQXsDu_ZEj0ydi__kwRkHsgw9bZW2-o-G4eMML6GiZG0eV9lroWlpGJPlz_nblO3Gn1tZkXPPRe-g/https%3A%2F%2Fscholar.google.com%2Fcitations%3Fuser%3DLO7LZ3oJ https://secure-web.cisco.com/1mvpNMRQKSP8FkYyfvVpb7eLS9lj8kZfszgSu9oRJQ8X5gT1o5EbOPN9_w0I95lz3bmOOhFKTa2yoVqxi7B3ZxSiDoHdeWmAqnJ6H2C4zZ0V-Dryb5Fpf5HJAloFFnAPsltFLGzloThFZvs6eFlGeVt7cSS1vWQsIhhM1FylufIpPjPqlNUy1L4AaJ6HlQtupYff3l2933LsgOOn6hPtplYjxT35EZg2jWOhSoBoJqYbI6T5McFyGjNG6_xmplW_nWwnr2nGkwIP7R2THKOSbB2oi_XpvElIQbTLyxgEOSjJaSbVmrbfjwXlAdkK5xx5iyvuPMc7Ki0qOdzWHpNM0Ew/https%3A%2F%2Fwww.researchgate.net%2Fprofile%2FGonzalo_Rojas2 https://secure-web.cisco.com/1BSQzDFZczyH2KnRdF2ICVDpUxz6g0ttdU0u-j9PVXo7bIp_PAiaidUZgqXnba0vu5Bcu80MTlDSLj_H7drSSmjw9o-ApoFWbGvavQaIPYZkWqEeyYHXffZDlBqPAfGOKiijJqECUGZQ0ZkgMjioihhpc_46unYRzJwP_Olaq_uOLxoBnFiOk7RIEOQOrq4m6ogPai73zS4t5-NWaw-Mn-m-7R5KlfS9by8_FWZHpa8Er7-QUKcjE38ltkwFIVoarGW9OvPw0N-crWzU8IYfcTPNe5bDV_hl0-6p7OS4tpeaMilAitHaZVfbxHEjfdo0qXAT3CbbKH9FEWORrybZ44Q/https%3A%2F%2Fcvn.fecyt.es%2F-0002-6228-2678 http://secure-web.cisco.com/1dOFt7henxwABk7hXay_AiRKApZWkzldFKpSeFu7YZA9mXuuq9U_88R1YuXngvPpHdu4VYrPFXW8qpV_t3rjlxPDrWmJNKmo7DIqMAcaKYwVd34QHt8Vu2frhBEQ5zp0hhEKyySjNS26mVbfna1FwRR2qFoO4GLoa0O-CUfmtFcpmQp1ZS5tB3IIIooNFaP9ioUIuL6frrXyXTu8HtC7ofXbWJekLulscwlodKoWS9-0rO63GYRLbZPq7ezoZNSITVOB6XKri_qCiUi8hy6OQd2arca-LWXt0BwR65j3RHAX2DYtTHt-hFCsLj9gxEGZppeokmXXZGI__MKC2zTaPkw/http%3A%2F%2Fwww.researcherid.com%2Frid%2FB-2036-2013 https://secure-web.cisco.com/1Th1b2nsH7DOoOS75firwrxXGmPTRXXCJK7nGZMWtY8MELWqNmHiJIS9tMuuGkwnYTZ9aJ15O9a5OeCMYTkOBAPIwIDNZjyO4qlCxeP18bVZa0AvP26wB6Qkdew8E7SeIKlwzJWNlh6zOfjaJO3m5Z-4JtKJdxdQGlOCiylUc1b9uoVLu836jxV38np5BFFUBTUXiqXiPHMJ4c-zCdHzMc2cH0X2THYKZG7S39ZW0lJvDZHwg7dYeDZZ6o4Xx08zkRjVR00HM35JJbEavZAQ2orYZuhSCzBQl4JG4DH-xQwa1qsm_N_RKSzTcQ26dMv7fiNbb3_KBGtQBzOCM8yU5aw/https%3A%2F%2Fcl.linkedin.com%2Fin%2Fgonzalorojascosta ___ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] "Vertex Talairach" in tksurfer?...
External Email - Use Caution Hi: "Vertex Talairach" in tksurfer: how does it relate to MNI coordinates? Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 https://secure-web.cisco.com/1jo94BTSUPIktp_eQAT5GZbTfpsA5KIpUTdHrT-g0xQG4-S9EJ8Se0bZ-x-FBmAHQvYIjWd9icohu9q2Pnb4rvuP2DUhhVKu7t5Wnhpjo9xP74g7qKTv6U0ChKq_-1FyQ5sebwrPR7VkGIIEyhf1UFV-zrGaJCJ4ACZPaSOZ3OdLQorGqisnmzfRcpR3JJB32HW4pkk7RGfgsJxAxLXLEk9OullOyfJzNEyUEoBWBxgUGRkd6KwOuXz5-np092RQdmjkD9QRN0a9foyUoKWUkRyOn7koc7RQHGHe03Fh92Rqu5Fi6CXUW5jwGZflR0GBnbCSbqstDlI4FEaP7_jsgzw/https%3A%2F%2Fscholar.google.com%2Fcitations%3Fuser%3DLO7LZ3oJ https://secure-web.cisco.com/13i-ZsZNcbWZqtgw0IQqpdq0G6AvtrIwdfNJ8UTQmrf8EhhJ2lCY1ZDJ-kezkBU0AAy_vv4Azuz33lpmU0ZbLA2nHUjidVv65CTcGSNTTvmV7nSszwXnbZUzdR4cxJNoKZfRhfejx55szDKhi_nzFiosIt9Eej83F0YSefai2-PyOr5xd_QIeWyFmls7S-DQeRtKqmnSp-RbZuKETfvJ4mWT9NSOvYnIhxCiobPUJFAGD7ZILZnU7bbnCiAjIBYv8yuSY5m-HVK-UiQQ3i5IS9rHovWaKN3DKlau_vmmKRZvEIuxP9YUOmfF8jSB2HQ0niL286YhAHWWKJco4cMR9VQ/https%3A%2F%2Fwww.researchgate.net%2Fprofile%2FGonzalo_Rojas2 https://secure-web.cisco.com/1nQ-nK1zgqFE9FeklGRmkE8GyAOu5VBkwnRcdrdjH0AT19qokDRNGC7dFLGHIJpu_uAQkB0ILQBfMxyMk_uKa3pHUwPtpmz7R8dPE9SY0hW44ej5QXIfU5D55jdlncq0917W-rK10jHFYJaUrkuh7k5DwKgFUsSQhfiLmLxGiEc3IzUaxOHk-KLz_EMH3CA8x9GX60gL8yUCrYI59FX1II-k2tNkmgpRidYs49GydHIPMDk06hNuyJ-UL0x52NHLOwI5Hq4kIl6fQ_rQZsnz5uQR8ZLRZkdRQKJbwEcPwO96Lv52U3vDqZVH8F0xOOGj8bD4M1TSPnbrLzqJGwmT3yg/https%3A%2F%2Fcvn.fecyt.es%2F-0002-6228-2678 http://secure-web.cisco.com/16_Ws70db2hTLXeCVLoJofARkDDcVXKV7r9SqYHL1F22JaHZhqn2_3AI8Z0jg16PjinIICTHayDODQa0NSxzU9F6gOUiYR-MjpSvWGqLSmJFi6_AmCb0KiFvXdMbPdbesi6lfXfc7AqpS8YapWwl_8WSqulYZ9O1xho6ln5QqrXlDCF8dPO9JNkz0VKR8PcdRjxQYp7TwqERfuSC09H8frc-pyWw_QCSDr2116wxYqylybIOll_-cGYEjKV65oDwqMnI29erzgzzoJb21rPxe4PSsypPorKis4li-FiLArM9Zt0CQG_pmm_FboJQAIKMPj9qAV6Pqz3napQNSv7TLLQ/http%3A%2F%2Fwww.researcherid.com%2Frid%2FB-2036-2013 https://secure-web.cisco.com/1Q9jZG4ZNnNMXhDtADVtnz_v3JI4jUseEVnhR7Yv-c6tC1QEfY9jwUedllpM0TwekpQHNV0qwFzM_oEeelUjzJIXAm0Ii2ahdKOCxrthg2zd3Lwwpb8c0xEDl6lO5DE3l6_kwHfYk2ue2L849vKXAb3WLvC1wp0yjppkItK1f5qPxTzkBiK8XfKN_QDzjc3OBhyGMJE4bo1vUvCHPZZYV9vnBXIOsHe5qN0c4cvNc1yejUMNsl68Zwjzh_mhbI0XZZgJSaVtEjFxe_mQ2q5MkX6mzRWltd-cCCfGoFJf1Vks-Ku-rslJ0FzCxMnazvLF_fS8L5h3lbECMDV4ZBgxo1Q/https%3A%2F%2Fcl.linkedin.com%2Fin%2Fgonzalorojascosta ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] MNI coordinates to vertex...
External Email - Use Caution Hi: I have MNI 152 coordinates equivalent to 10-10 and 10-20 EEG electrodes (see Supplementary Tables 1 and 2 in paper https://secure-web.cisco.com/1h63DivIA2LKRlpONd2jZm_aVQOA0BCPi_yLJr4IOlwxEnAfG08DTJr4RESN6HNnmpW3-E_UvbeM3gHrvz45Ffp-ub6J_Np6lfVtQ-urfy0CTi7672EBA_mLrRAia7mNvzT68y_guei851pm1d8XV2cR1RSDalXLHDA9Ke5sLgFL6Fh9Yl4Wksvf4yv5m9vKUX78O0zaqcsra4y_lXRM6WmYSyunCln8zq-o4zhHpOJi9mxMv94gkFL3W6Qq15IgevuZW2DszvH0qldFuO7Zs1mlqtqPX6x3W7fboWEP7YNU6uWqQjw83SQ-eVoqP08b8nr9GPt7YWnQiEmuuv2RxoGsBBsXsp5oZCXYj-4vd-so/https%3A%2F%2Fwww.frontiersin.org%2Farticles%2F10.3389%2Ffnins.2018.00235%2Ffull How to convert that MNI coordinates to vertex in the pial surface ? Sincerely Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 http://secure-web.cisco.com/15G7UB7H3xj-A5kT53KhLNPISazwoqZ-keP4CKddUdONSzaclrTW_4kL1gzfT5LCKNIxW20vH_QDHco5kmYLttqUu4e8jkW3JBW9DUsDoB9f9SOMs1mn1dD59eELilCW1LhACz1VJFO4E3dQ26tunuZc6D__DRIhe9fgD6JoE0iItwqSNg68NeZ4RASD7W4Pjyg9_KKj5NbqLbhLa8RPca-8_aEPD5qVZpt4x29p_RdJXgBJXHUHhdBRgSy_aPisJG6AGKdRU0epYbLtpo8y464gCRbB5VghLFXymitvnyeGVOinJGNpoLqhSLgZjIA1PQXyC139hk1AJgj48yzgw7uaL-6_k8xo4t57RNrH4vvM/http%3A%2F%2Fwww.aribrain.info https://secure-web.cisco.com/12viTch2L-4x6NKy94c7WpcDwZ3HTM2I3oGRkhAsSGTmNzRuLrWMre0roGFkNYPXgfEFN5UK2TR4T8TzBi4hnXspOKMTqariKk1mtzvgSvU-xElxHDlGTHEOIJcGd3bHpJr9RnbFo-QDPhp9-xwx50WCSrt6Z0UwPY5q_n9TLmJz8WnCCypDdOxiIZTc9m7V6_QxoOYckLxVXynvGv9oTwi9BpJd4Q9QyPktuVpqoqwiJciei0H_exjpoTYcC0ir4DilEoAxhbsbflYlw5zkqJyre04NapU8n4bgTSAtvormsXKHKM5ose5DYmYhNWxpV3rNTam-tnluow0CppMnr53AU6wXpLFnajgL7v931VQI/https%3A%2F%2Fscholar.google.com%2Fcitations%3Fuser%3DLO7LZ3oJ https://secure-web.cisco.com/1j6d3d9sra7KYe340OH3hwmLgVbtcqgErcrjhSz4FftpTgnFGlU5_trTzKl45lLTOd3xzTf29VPg8z_gt9tw1Dh3gCm9Uze9UwpFu5sv3fU2MMXgKhEd5jcYKLYCoXGAf7ajPhxdH0shJ81HKoMNidsTttC1fg94RL86fO0WF7hcySaFbRd-byI2XZCb_z7IZr1SUoGWQfnB1zOPenPCwkJJGJqduw29VSs_4IqfPb1HN_ZiEpFx7GK3xLxYAoercPTASBL6xAdDEPxPwv5W1hoYN907Z5uplNdOPPRF26dKpncsphBpr2syrCty84at8tmvDKbRfGwDlqBs88_-WVTDIOJ7RfRVI6IWe-xZZVmw/https%3A%2F%2Fwww.researchgate.net%2Fprofile%2FGonzalo_Rojas2 https://secure-web.cisco.com/1U5osbupkYDzRTSQetIvNibKkd020KxYF82vGNYJMRCBn6EaMkJAt3povDfYEQw8SdWmNQpcYhNBuptWVORc5j9AjY4xlGuH68OzQzrALAk8OgbOnm73LmPoQkcx85iu6HxBdwz7-0BbiVl_5WZMTP91WvUPEmOAqMLE4lxqAn17zP6p95pL1CQBpyfQJFKuCGWrT9jpn0-5I_unsvHYB8bz59ZcJKbV1Di5BlA79Qg7ZMyoKMmjWziMzzWJsFVA1JANAQERn8QEGZXKNlsKysBwtfoZi4av39cWIE2QevqeV75Vn6znPC9q2sb3tGFSVtsIbSo5YbYg7Tju_fmiQZ0yy175RiBLuzAmCTOV9U7s/https%3A%2F%2Fcvn.fecyt.es%2F-0002-6228-2678 http://secure-web.cisco.com/14Rn0C97f3SuE-gY9gJeCiBXYhQ9pvBuNH5M-itIL_uLqiIcf9TR3MaKZjQzouiU2NUd1BFnyODYC1p1vaQf4iiqU3gnfyN-y-P-uEY9GhxgcemTtEYQFhtKwNgdyi278Uv3uVS0z1lvmnkpcU46Pl98P_3-LPKGWwo7bG2wWJmJqsJMbLCNwtrjaTf5T00vi5yZaq-n0PjHySUOAzB8igAz8WrX1uFvZWjVEW4aWaOU5NetNVHSmGXPt6muiN7PUwia8Bz3tPt7skUZyzOFHQ1-LQnOf9Cc4FEjXx0oLJuQMxxaGyRDkoKrSqVK4Z0rc4MIbYeR1Je63lufoIuqK0mY9bq6RsLT_7jxsj57GABw/http%3A%2F%2Fwww.researcherid.com%2Frid%2FB-2036-2013 https://secure-web.cisco.com/1DJcTJuO0lQGWBymluz9_ARIefxo929bzOP041a22SpnJKfsZxYOT3wvibdWbe6wKCe0NZQV6KcIYfNVm9j7ituFUIPSdAueDt6zvgEu4qnaP5zkSQeq60coCvB-DAbcQnhqeJV633BSH-IUp9f5PmUWyrrCcTQJaNwGDfLnHKYWnNWo6S4N7GFZjDJ3-94yCA8v29Lvnob0E3EZnMpdAteHMxlRRFE9hZZEaTimO8OvNmuqwg8-HhpON0cH8qCSrzO9aXZwoYj27mxxBEnSPKh7G5yDVzmxylhVvff8RdCQGaNzh1zsXIjfFRSpSElJUY8FtMyTtgBrPIQnkocbCyTA0dG8INeEPhOL5dfSbbKs/https%3A%2F%2Fcl.linkedin.com%2Fin%2Fgonzalorojascosta ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] resolution greater than 1 mm segmentation
External Email - Use Caution Hi: I know that using an mprage image with greater than 1 mm resolution, freesurfer converts it to 1 mm previous segmentation. There is any option that freesurfer uses the original resolution of the image? Any other software that do such a thing ? Especially hippocampal segmentation. Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Best mesh generation from hippocampus aseg segmentation
External Email - Use Caution Hi: Which is the best library or software to create the hippocampus mesh from aseg segmentation? Sincerely Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] virtual disk image of freesurfer 7.1.1
External Email - Use Caution Hi: Where can I find the virtual disk image of freesurfer 7.1.1 ? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] big difference between ICV same patient....
External Email - Use Caution Hi: I modified the coregistration using "tkregister2 --s subj1 --fstal --surfs". Then, I used "recon-all -make all -s subj1", but I got "Nothing to be done"... why ?... Which command must I run after tkregister2 to reprocess ? Other question... what do you mean with " You might be comparing dewarped vs not dewarped" Sincerely, Gonzalo Rojas Costa >Message: 6 >Date: Thu, 10 Sep 2020 12:42:41 -0400 >From: "Douglas N. Greve" >Subject: Re: [Freesurfer] big difference between ICV same patient >To: >Message-ID: <0112a2be-2c41-a100-6ac7-e8d054e97...@mgh.harvard.edu> >Content-Type: text/plain; charset="utf-8" > >It all comes down to the registration. See >https://surfer.nmr.mgh.harvard.edu/fswiki/eTIV >The image may have more-or-less neck and that can change the >registration and ICV. The contrast may be different. The scanner may >have had software updates. You might be comparing dewarped vs not dewarped. > >On 9/10/2020 2:16 PM, Gonzalo Rojas Costa wrote: >> >> External Email - Use Caution >> >> Hi: >> >> ? Why I got a big ICV difference between MPRAGE of the same patient >> (2019: 1775887.317631, 2020: 1566398.53576 mm3), one-year difference >> acquisition, and the same MRI Skyra 3T equipment? I used freesurfer >> 5.1.0 on the same computer, and operating system in both cases... >> >> ? I reviewed the coregistration to MNI305 and it is reasonably good in >> both cases... >> >> ? The case was reviewed by an expert neuroradiologist, and she does >> not consider that there is a significant visual difference between >> both sizes. >> >> ? Sincerely >> >> >> >> Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] big difference between ICV same patient....
External Email - Use Caution Hi: Why I got a big ICV difference between MPRAGE of the same patient (2019: 1775887.317631, 2020: 1566398.53576 mm3), one-year difference acquisition, and the same MRI Skyra 3T equipment? I used freesurfer 5.1.0 on the same computer, and operating system in both cases... I reviewed the coregistration to MNI305 and it is reasonably good in both cases... The case was reviewed by an expert neuroradiologist, and she does not consider that there is a significant visual difference between both sizes. Sincerely Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] freesurfer 7.0.0 in a virtual machine...
External Email - Use Caution Hi: No... I don't have any specific issue... I have a previous freesurfer version installed that I want to continue using. So I want to install version freesurfer 7.0 on a virtual machine... Sincerely, Gonzalo Rojas Costa > Message: 4 > Date: Thu, 7 May 2020 12:43:56 +0200 (CEST) > From: Tim Sch?fer > Subject: Re: [Freesurfer] freesurfer 7.0.0 in a virtual machine... > To: Freesurfer support list > Message-ID: <1445340988.123994.1588848236...@ox.hosteurope.de> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > There should be no difference to installation on a physical machine. Are you > running into any specific issues? > > Tim > >> On May 7, 2020 at 3:51 AM Gonzalo Rojas Costa < gonzalo.rojas.co...@gmail.com> wrote: >> >> >> External Email - Use Caution >> >> Hi: >> >> How can install freesurfer 7.0.0 in a virtual machine ? >> >> Sincerely, >> >> >> Gonzalo Rojas Costa >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >-- > Dr. Tim Sch?fer > Postdoc Computational Neuroimaging > Department of Child and Adolescent Psychiatry, Psychosomatics and > Psychotherapy > University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] freesurfer 7.0.0 in a virtual machine...
External Email - Use Caution Hi: How can install freesurfer 7.0.0 in a virtual machine ? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] libpng12.so.0
External Email - Use Caution Hi: I tried to use the tkregisterfv command in Ubuntu 18.04.4 LTS, but I got the following error: "freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory". How can I solve it ? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FreeSurfer 6.0 disk image for VirtualBox?
External Email - Use Caution Hi: Where can I find the FreeSurfer 6.0 disk image for VirtualBox? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] library to show freesurfer data embedded in a web page (mesh and axial, coronal, sagital slices)
External Email - Use Caution Hi: Do you know any library that allows to show freesurfer generated data (mesh and axial, coronal, sagittal slices) embedded in a web page? We were working using "BrainBrowser Volume Viewer" (brainbrowser.cbrain.mcgill.ca) and "AMI Medical Imaging (AMI) JS Toolkit" (https://fnndsc.github.io/ami), but I have some problems... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] web page library to show freesurfer data (mesh and axial, coronal, sagital slices)
External Email - Use Caution Hi: Do you know any library to show freesurfer data (mesh and axial, coronal, sagittal slices) embedded a web page? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Cortical thickness values more than 5 mm
External Email - Use Caution Hi: How can I get cortical thickness surface image with values more than 5 mm? Sincerely Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] cortical thickness values in the insula...
External Email - Use Caution Hi: How can I get the different values of cortical thickness in the insula? Not the mean and SD... Sincerely Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] curved reformat image....
External Email - Use Caution Hi: How can I get in an automatic way curved reformat images (for example, see paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5009174/) Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl http://www.aribrain.info https://scholar.google.com/citations?user=LO7LZ3oJ https://www.researchgate.net/profile/Gonzalo_Rojas2 https://cl.linkedin.com/in/gonzalorojascosta ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] "CorticalWhiteMatterVol" ?
External Email - Use Caution Hi: What is the meaning of the "CorticalWhiteMatterVol" measure? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] myelination and freesurfer segmentation...
External Email - Use Caution Hi: Could you please tell me if Is there is a paper on myelination and segmentation? Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl http://www.aribrain.info https://scholar.google.com/citations?user=LO7LZ3oJ https://www.researchgate.net/profile/Gonzalo_Rojas2 https://cl.linkedin.com/in/gonzalorojascosta ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] local Gyrification Index
Hi: To compute local Gyrification Index is necessary Matlab... Complete installation or only runtime? Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl http://www.aribrain.info https://scholar.google.com/citations?user=LO7LZ3oJ https://www.researchgate.net/profile/Gonzalo_Rojas2 https://cl.linkedin.com/in/gonzalorojascosta ___ 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] lobes volume (WM and GM)
Hi Douglas: I am looking for that paper, but I couldn't found it... Which is it ? Sincerely, Gonzalo Rojas Costa Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl http://www.aribrain.info https://scholar.google.com/citations?user=LO7LZ3oJ https://www.researchgate.net/profile/Gonzalo_Rojas2 https://cl.linkedin.com/in/gonzalorojascosta On Thu, Sep 21, 2017 at 6:21 PM, Douglas N Greve wrote: > No, not for lobe volume. Have you seen the original wmparc paper? > > > > On 09/20/2017 04:53 PM, Gonzalo Rojas Costa wrote: >> >> Hi Douglas: >> >>I am looking for papers that used the volume of each lobe computed >> using freesurfer, but I couldn't found it... Do you know any?... >> >>Sincerely, >> >> >> Gonzalo Rojas Costa >> Laboratory for Advanced Medical Image Processing >> Department of Radiology >> Clínica las Condes >> Lo Fontecilla 441, Las Condes, Santiago, Chile. >> Tel: 56-2-2105170 >> Cel: 56-9-97771785 >> www.clc.cl >> http://www.aribrain.info >> https://scholar.google.com/citations?user=LO7LZ3oJ >> https://www.researchgate.net/profile/Gonzalo_Rojas2 >> https://cl.linkedin.com/in/gonzalorojascosta >> >> >> On Wed, Sep 20, 2017 at 5:47 PM, Douglas N Greve >> wrote: >>> >>> We did not have a strong reason, just that it seemed to give maps that >>> looked reasonable >>> >>> >>> >>> On 09/20/2017 04:42 PM, Gonzalo Rojas Costa wrote: >>>> >>>> Hi Douglas: >>>> >>>> Why you specified 5mm as the default value for the --wmparc-dmax >>>> option in mri_aparc2aseg command? >>>> >>>> Sincerely, >>>> >>>> >>>> Gonzalo Rojas Costa >>>> Laboratory for Advanced Medical Image Processing >>>> Department of Radiology >>>> Clínica las Condes >>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>> Tel: 56-2-2105170 >>>> Cel: 56-9-97771785 >>>> www.clc.cl >>>> http://www.aribrain.info >>>> https://scholar.google.com/citations?user=LO7LZ3oJ >>>> https://www.researchgate.net/profile/Gonzalo_Rojas2 >>>> https://cl.linkedin.com/in/gonzalorojascosta >>>> >>>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> >>> >>> The information in this e-mail is intended only for the person to whom it >>> is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >> >> > > -- > 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
Re: [Freesurfer] lobes volume (WM and GM)
Hi Douglas: I am looking for papers that used the volume of each lobe computed using freesurfer, but I couldn't found it... Do you know any?... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl http://www.aribrain.info https://scholar.google.com/citations?user=LO7LZ3oJ https://www.researchgate.net/profile/Gonzalo_Rojas2 https://cl.linkedin.com/in/gonzalorojascosta On Wed, Sep 20, 2017 at 5:47 PM, Douglas N Greve wrote: > We did not have a strong reason, just that it seemed to give maps that > looked reasonable > > > > On 09/20/2017 04:42 PM, Gonzalo Rojas Costa wrote: >> >> Hi Douglas: >> >>Why you specified 5mm as the default value for the --wmparc-dmax >> option in mri_aparc2aseg command? >> >>Sincerely, >> >> >> Gonzalo Rojas Costa >> Laboratory for Advanced Medical Image Processing >> Department of Radiology >> Clínica las Condes >> Lo Fontecilla 441, Las Condes, Santiago, Chile. >> Tel: 56-2-2105170 >> Cel: 56-9-97771785 >> www.clc.cl >> http://www.aribrain.info >> https://scholar.google.com/citations?user=LO7LZ3oJ >> https://www.researchgate.net/profile/Gonzalo_Rojas2 >> https://cl.linkedin.com/in/gonzalorojascosta >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] lobes volume (WM and GM)
Hi Douglas: Why you specified 5mm as the default value for the --wmparc-dmax option in mri_aparc2aseg command? Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl http://www.aribrain.info https://scholar.google.com/citations?user=LO7LZ3oJ https://www.researchgate.net/profile/Gonzalo_Rojas2 https://cl.linkedin.com/in/gonzalorojascosta ___ 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] lobes volume (WM and GM)
Hi Douglas: By removing --rip-unknown I got the same results... Why ?... Sincerely, Gonzalo Rojas Costa > Date: Tue, 12 Sep 2017 12:33:11 -0400 > From: Douglas N Greve > Subject: Re: [Freesurfer] lobes volume (WM and GM) > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > Content-Type: text/plain; charset=utf-8; format=flowed > > Try removing the --rip-unknown > > > On 09/12/2017 11:09 AM, Gonzalo Rojas Costa wrote: >> Hi: >> >>I created the following script (for freesurfer 5.3.0) to compute the >> lobes volume (including GM and WM). >> >>mri_annotation2label --subject pac --hemi rh --lobesStrict lobulos >> --seg lobulos --stat lobulos >>mri_annotation2label --subject pac --hemi lh --lobesStrict lobulos >> --seg lobulos --stat lobulos >>mris_anatomical_stats -a lobulos -f pac.lobulos.rh pac rh >>mris_anatomical_stats -a lobulos -f pac.lobulos.lh pac lh >>mri_aparc2aseg --s pac --labelwm --hypo-as-wm --rip-unknown >> --volmask --o $SUBJECTS_DIR/pac/mri/lobulitos.mgz --annot lobulos >> --wmparc-dmax 20 >>mri_segstats --seg $SUBJECTS_DIR/pac/mri/lobulitos.mgz --ctab >> /usr/local/freesurfer/LobulesColorLUT.txt --excludeid 0 --sum >> $i.lobulo.aseg.sum --id 1001 1004 1005 1006 2001 2004 2005 2006 3001 >> 3004 3005 3006 4001 4004 4005 4006 251 252 253 254 255 >> >>But, I didn't got the complete WM volume for each lobe (frontal lobe >> for example... see red arrow in attached image)... why ?... Any >> solution ?... >> >>Sincerely, >> >> >> Gonzalo Rojas Costa >> Laboratory for Advanced Medical Image Processing >> Department of Radiology >> Cl?nica las Condes >> Lo Fontecilla 441, Las Condes, Santiago, Chile. >> Tel: 56-2-2105170 >> Cel: 56-9-97771785 >> www.clc.cl >> http://www.aribrain.info >> https://scholar.google.com/citations?user=LO7LZ3oJ >> https://www.researchgate.net/profile/Gonzalo_Rojas2 >> https://cl.linkedin.com/in/gonzalorojascosta >> >> >> ___ >> 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] lobes volume (WM and GM)
Hi: I need the complete WM volume for each lobe... not only the WM up to 5mm beneath the lobes (default value) or 20 mm... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl http://www.aribrain.info https://scholar.google.com/citations?user=LO7LZ3oJ https://www.researchgate.net/profile/Gonzalo_Rojas2 https://cl.linkedin.com/in/gonzalorojascosta ___ 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] volumetric difference between 1.5 T and 3.0 T...
Hi: There exist any difference between the volumetric values obtained using 1.5T and 3.0T images ? Any paper about it ? Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] Freesurfer Digest, Vol 141, Issue 22
Hi Martin: But, between version 5.3 and 6.0 there are any differences in the algorithms for subcortical volume, cortical thickness, etc., or only additions to that, such as the hippocampus or brainstem subfields ?... and in general, if I segment for example the same healthy control in freesurfer 5.3 and 6.0 in the same operating system, there will be any difference in subcortical volumes and/or cortical thickness ?... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl On Wed, Nov 11, 2015 at 7:57 AM, wrote: > -- > > Message: 24 > Date: Tue, 10 Nov 2015 16:57:43 -0500 > From: Martin Reuter > Subject: Re: [Freesurfer] 5.3 vs 6.0 volumetric differences... > To: Freesurfer support list > Message-ID: <56426857.3030...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > Hi Gonzalo, > > of course. > > There is even a difference when running the same FS version with a > different operating system (due to differences in the numerical > libraries, optimizations etc). > > Are changes big or small? > In a single case they can be very big (it could be a case that failed in > 5.3 and works with 6.0 - or the other way) > > Are changes directional (significantly larger or smaller volumes/thickness)? > Hard to say and hard to detect if small, but it can happen due to a new > algorithm that measurements are consistently larger (/smaller) than in > another version. We try to avoid this, but it can theoretically happen. > > That is why it is so important to stick with the same version and > operating system when processing data. > > Best, Martin > > On 11/10/2015 04:48 PM, Gonzalo Rojas Costa wrote: >> Hi: >> >>There are any difference between subcortical structures volume, >> cortical thickness, supratentorial volume, gray matter volume, etc. >> computed with freesurfer 5.3 and 6.0 ?... >> >>Sincerely, >> >> >> Gonzalo Rojas Costa >> > > -- > Martin Reuter, PhD > Assistant Professor of Radiology, Harvard Medical School > Assistant Professor of Neurology, Harvard Medical School > A.A.Martinos Center for Biomedical Imaging > Massachusetts General Hospital > Research Affiliate, CSAIL, MIT > Phone: +1-617-724-5652 > Web : http://reuter.mit.edu ___ 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] 5.3 vs 6.0 volumetric differences...
Hi: There are any difference between subcortical structures volume, cortical thickness, supratentorial volume, gray matter volume, etc. computed with freesurfer 5.3 and 6.0 ?... Sincerely, Gonzalo Rojas Costa -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] 1.5T vs 3.0T longitudinal study...
Hi: I have two timepoints of the same patient: the first is in 1.5T and the second in 3.0T... Is it possible to do the longitudinal study (subcortical volumes) using the Workflow Summary described in https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing ?... Sincerely, Gonzalo Rojas Costa -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clinica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] comparison of subcortical volume with 1.5 T and 3T...
Hi: I have some longitudinal study of a patient with 1.5 T images... now, we have 3T mprage images of the same patient... how can I do the comparison of the subcortical volume of the patient ?... Sincerely, Gonzalo Rojas Costa -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] options for 7T images...
Hi: Must I use any recon-all option for 7T images ?... Sincerely, Gonzalo Rojas Costa -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] Ubuntu 14.04 LTS 64 bits
Hi: Which freesurfer version must I install in Ubuntu 14.04 LTS 64 bits ?... Sincerely... Gonzalo Rojas Costa -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] Longitudinal study: analyze results
Hi: For example: if I want to compare the volume of left hyppocampus in two time points, could I compare the volume in aseg.stats file of both "long" folders?... Sincerely, Gonzalo Rojas Costa -------- Gonzalo Rojas Costa Advanced Medical Image Processing Laboratory Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] Longitudinal study... analyze of results....
Hi: I want to do a longitudinal study between two time points of a patient... I want to compare the volume of the hypocampii, white matter, etc... I did the computation of both time points, I created the "base" image, and the "long" ones... How can I analyze the aseg.stats files in each "long" folder ?... Sincerely, Gonzalo Rojas Costa ------------ Gonzalo Rojas Costa Advanced Medical Image Processing Laboratory Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] Longitudinal difference...
Hi: We have GE 1.5T MRI fspgr volumetric acquisition of a MS patient (39 years old) and a Siemens 3T MRI mprage acquisition of the same patient three years after (42 years old)... we processed that images to got the volume of some structures that we need and compare... but, we found that multiple brain structures are bigger in the 42 year old images: right hypocampus (3187-3755), right cerebral white matter (151164-172448), right Cerebellum-White-Matter (12652-14902), right Cerebellum-Cortex (48812-51935), etc... And a similar situation occurs in left hemisphere... The Intracranial volumen in both cases is: 1348899,976 and 1332590,755197... Why is the difference in volumen in the structures in both studies ?... Why is always bigger at 42 years old than 39 years old?... Any technical problem ?... We got a similar difference by normalizing with ICV... Sincerely, Gonzalo Rojas Costa ___ 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] Nframes greater than 1...
Hi: I don't know it is an mprage got in our center using a Siemens Avanto equipment freesurfer specify that the images has two nframes and for that reason freesurfer could not process it... Sincerely Gonzalo Rojas Costa >Hi Gonzalo > >what is in the two frames? >Bruce >On Tue, 2 Sep 2014, Gonzalo Rojas Costa wrote: > >> >> Hi: >> >> I have an mprage image with nframes = 2... how >>can I convert it to use it in >> freesurfer ?... >> >> Sincerely, >> >> Gonzalo Rojas Costa Gonzalo Rojas Costa Advanced Medical Image Processing Laboratory Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] Nframes greater than 1...
Hi: I have an mprage image with nframes = 2... how can I convert it to use it in freesurfer ?... Sincerely, Gonzalo Rojas Costa Gonzalo Rojas Costa Advanced Medical Image Processing Laboratory Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] Pons and midbrain segmentation....
Hi: How can I segment the pons and midbrain using freesurfer ?... or any other segmentation software that do such task ?... Sincerely, Gonzalo Rojas Costa Gonzalo Rojas Costa Advanced Medical Image Processing Laboratory Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] Generation of brodmann area label and statistics..
Hi Bruce; Thanks you very much... It rans ok... Sincerely, Gonzalo Rojas Costa Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl El nov 15, 2013 11:12 AM, "Bruce Fischl" escribió: > Hi Gonzalo > > recon-all -s -balabels > > should do the trick > > cheers > Bruce > On Fri, 15 Nov 2013, Gonzalo Rojas Costa wrote: > > >> Hi: >> >> I have some freesurfer processed studies I used 5.1 version, and now I >> found that it don't has the brodmann area labels and statistics generated >> in >> some studies... How can I create it without doing again the complete >> recon-all ? >> >> Sincerely, >> >> >> Gonzalo Rojas Costa >> Laboratory for Advanced Medical Image Processing >> Department of Radiology >> Cl?nica las Condes >> Lo Fontecilla 441, Las Condes, Santiago, Chile. >> Tel: 56-2-2105170 >> Cel: 56-9-97771785 >> www.clc.cl >> >> >> >> > > 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] Generation of brodmann area label and statistics..
Hi: I have some freesurfer processed studies I used 5.1 version, and now I found that it don't has the brodmann area labels and statistics generated in some studies... How can I create it without doing again the complete recon-all ? Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] Newest freeview version...
Hi: Which is the freeview newest version ?... the one that is included in freesurfer 5.3.0 package ?... Sincerely, Gonzalo Rojas Costa Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] (no subject)
Hi: Which is the optimal parameters for a morphometric sequence (fspgr?) n a 1.5 T MR OPTIMA 450w GE MRI equipment ?... Because, we are using an fspgr 1mm isotropic sequence, but we got wrong defined borders in some structures... for example, hypocampus, cortex-wm... I think it could be because the GE images appears smoothed in comparison with the Siemens Avanto mprage images that we also use... Any comments ? Sincerely, Gonzalo Rojas Costa Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] a second "subjcts" folder...
Hi: I has a "subjects" folder in one physical harddisk... How can I continue processing more images in another "subjects" folder in a new physical harddisk without erasing the first one ?... Sincerely Gonzalo Rojas Vosta -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] white matter volume per lobe...
Hi Douglas: The file is the OAS1_0001_MR1 case of OASIS-BRAINS database that I re-processed using freesurfer 5.2.0... Sincerely, Gonzalo Rojas Costa On Fri, May 31, 2013 at 12:12 PM, Douglas N Greve wrote: > don't know what's going on. Can you upload the subject to our file drop? > doug > > On 05/30/2013 04:36 PM, Gonzalo Rojas Costa wrote: >> >> Hi Doug: >> >>The command is: >> >> mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown >> --volmask --o mri/lobulitos.mgz --annot lobulos --wmparc-dmax 200 >> >> and the terminal output is: >> >> mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown >> --volmask --o mri/lobulitos_2.mgz --annot lobulos --wmparc-dmax 200 >> >> SUBJECTS_DIR /usr/local/freesurfer/subjects >> subject OAS1_0001_MR1 >> outvol mri/lobulitos_2.mgz >> useribbon 0 >> baseoffset 0 >> labeling wm >> labeling hypo-intensities as wm >> dmaxctx 200.00 >> RipUnknown 1 >> >> Reading lh white surface >> /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/lh.white >> >> Reading lh pial surface >> /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/lh.pial >> >> Loading lh annotations from >> /usr/local/freesurfer/subjects/OAS1_0001_MR1/label/lh.lobulos.annot >> reading colortable from annotation file... >> colortable with 8 entries read (originally none) >> >> Reading rh white surface >> /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/rh.white >> >> Reading rh pial surface >> /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/rh.pial >> >> Loading rh annotations from >> /usr/local/freesurfer/subjects/OAS1_0001_MR1/label/rh.lobulos.annot >> reading colortable from annotation file... >> colortable with 8 entries read (originally none) >> Have color table for lh white annotation >> Have color table for rh white annotation >> Loading ribbon segmentation from >> /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/ribbon.mgz >> Loading filled from >> /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/filled.mgz >> Ripping vertices labeled as unkown >> Ripped 7659 vertices from left hemi >> Ripped 7544 vertices from right hemi >> >> Building hash of lh white >> >> Building hash of lh pial >> >> Building hash of rh white >> >> Building hash of rh pial >> >> Loading aseg from >> /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/aseg.mgz >> ASeg Vox2RAS: --- >> -1.000 0.000 0.000 128.000; >> 0.000 0.000 1.000 -128.000; >> 0.000 -1.000 0.000 128.000; >> 0.000 0.000 0.000 1.000; >> - >> >> Labeling Slice >>0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 >> 18 19 >> 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 >> 38 39 >> 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 >> 58 59 >> 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 >> 78 79 >> 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 >> 98 99 >> 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 >> 118 119 >> 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 >> 138 139 >> 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 >> 158 159 >> 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 >> 178 179 >> 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 >> 198 199 >> 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 >> 218 219 >> 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 >> 238 239 >> 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = >> 688931 >> Used brute-force search on 139 voxels >> Fixing Parahip LH WM >>Found 0 clusters >> Fixing Parahip RH WM >>Found 0 clusters >> Writing output aseg to mri/lobulitos_2.mgz >> >>Sincerely, >> >> >> Gonzalo Rojas Costa >> >> >> On Thu, May 30, 2013 at 4:10 PM, Douglas N Greve >> wrote: >>> >>> can you send me your full command line as well as the terminal output? >>> >>> On 05/30/2013 02:26 PM, Gonzalo Rojas Costa wrote: >>>> >>>> Hi Doug: >>>> >>>> But, in the mri_aparc2aseg command, I test with the "--wmparc-
Re: [Freesurfer] white matter volume per lobe...
Hi Doug: The command is: mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/lobulitos.mgz --annot lobulos --wmparc-dmax 200 and the terminal output is: mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/lobulitos_2.mgz --annot lobulos --wmparc-dmax 200 SUBJECTS_DIR /usr/local/freesurfer/subjects subject OAS1_0001_MR1 outvol mri/lobulitos_2.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 200.00 RipUnknown 1 Reading lh white surface /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/lh.white Reading lh pial surface /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/lh.pial Loading lh annotations from /usr/local/freesurfer/subjects/OAS1_0001_MR1/label/lh.lobulos.annot reading colortable from annotation file... colortable with 8 entries read (originally none) Reading rh white surface /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/rh.white Reading rh pial surface /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/rh.pial Loading rh annotations from /usr/local/freesurfer/subjects/OAS1_0001_MR1/label/rh.lobulos.annot reading colortable from annotation file... colortable with 8 entries read (originally none) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/ribbon.mgz Loading filled from /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/filled.mgz Ripping vertices labeled as unkown Ripped 7659 vertices from left hemi Ripped 7544 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/aseg.mgz ASeg Vox2RAS: --- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; - Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 688931 Used brute-force search on 139 voxels Fixing Parahip LH WM Found 0 clusters Fixing Parahip RH WM Found 0 clusters Writing output aseg to mri/lobulitos_2.mgz Sincerely, Gonzalo Rojas Costa On Thu, May 30, 2013 at 4:10 PM, Douglas N Greve wrote: > can you send me your full command line as well as the terminal output? > > On 05/30/2013 02:26 PM, Gonzalo Rojas Costa wrote: >> >> Hi Doug: >> >>But, in the mri_aparc2aseg command, I test with the "--wmparc-dmax >> 200" option... I put that big value to test it, but I got the image >> that I sent you... >> >>Sincerely, >> >> >> Gonzalo Rojas Costa -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] white matter volume per lobe...
Hi Doug: But, in the mri_aparc2aseg command, I test with the "--wmparc-dmax 200" option... I put that big value to test it, but I got the image that I sent you... Sincerely, Gonzalo Rojas Costa On Thu, May 30, 2013 at 12:06 PM, Douglas N Greve wrote: > > It is probably the region that is more than 5mm away from cortex. In the > wmparc it should be labeled as wm-lh-unknown > > doug > > > On 05/30/2013 11:27 AM, Gonzalo Rojas Costa wrote: >> >> Hi Doug: >> >>I used the instructions that you told me to get the white matter per >> each lobule... But, I got the grey colored region (red arrow)... Which >> neuroanatomical area is ?... >> >>Sincerely, >> >> >> Gonzalo Rojas Costa >> >> >>> Message: 15 >>> Date: Mon, 27 May 2013 22:41:41 -0400 >>> From: Douglas Greve >>> Subject: Re: [Freesurfer] white matter volume per lobe... >>> To: freesurfer@nmr.mgh.harvard.edu >>> Message-ID: <51a41965.6050...@nmr.mgh.harvard.edu> >>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>> >>> you will need to run mri_annotation2label and specify the output to be >>> an annotation file instead of a segmentation. Then you will have to run >>> mri_aparc2aseg, specifying your lobes annotation as well as --labelwm >>> (look in the recon-all.log file for an example of how wmparc.mgz is >>> created). Then run mri_segstats (you can also get an example from the >>> recon-all.log file). >>> doug >> >> -- >> Gonzalo Rojas Costa >> Laboratory for Advanced Medical Image Processing >> Department of Radiology >> Clínica las Condes >> Lo Fontecilla 441, Las Condes, Santiago, Chile. >> Tel: 56-2-2105170 >> Cel: 56-9-97771785 >> www.clc.cl > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] white matter volume per lobe...
Hi Doug: It is labeled as wm-rh-fusiform and wm-lh-fusiform Sincerely, Gonzalo Rojas Costa On Tue, May 28, 2013 at 1:47 PM, Douglas N Greve wrote: > what is is labled? > > On 05/28/2013 01:42 PM, Gonzalo Rojas Costa wrote: >> >> Hi Doug: >> >>I use the instructions that you told me... But, why I get the gray >> colored region (red arrow) ?... >> >>Sincerely, >> >> >> Gonzalo Rojas Costa >> >> >>> Message: 15 >>> Date: Mon, 27 May 2013 22:41:41 -0400 >>> From: Douglas Greve >>> Subject: Re: [Freesurfer] white matter volume per lobe... >>> To: freesurfer@nmr.mgh.harvard.edu >>> Message-ID: <51a41965.6050...@nmr.mgh.harvard.edu> >>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>> >>> you will need to run mri_annotation2label and specify the output to be >>> an annotation file instead of a segmentation. Then you will have to run >>> mri_aparc2aseg, specifying your lobes annotation as well as --labelwm >>> (look in the recon-all.log file for an example of how wmparc.mgz is >>> created). Then run mri_segstats (you can also get an example from the >>> recon-all.log file). >>> doug >> >> -- >> Gonzalo Rojas Costa >> Laboratory for Advanced Medical Image Processing >> Department of Radiology >> Clínica las Condes >> Lo Fontecilla 441, Las Condes, Santiago, Chile. >> Tel: 56-2-2105170 >> Cel: 56-9-97771785 >> www.clc.cl > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] white matter volume per lobe...
Hi: I used the following commands to get the cortical volume per each lobe: mri_annotation2label --subject OAS1_0001_MR1 --hemi rh --lobesStrict lobulos --seg lobulos --stat lobulos mri_annotation2label --subject OAS1_0001_MR1 --hemi lh --lobesStrict lobulos --seg lobulos --stat lobulos mris_anatomical_stats -a lobulos -f OAS1_0001_MR1_lobulos_rh -b OAS1_0001_MR1 rh mris_anatomical_stats -a lobulos -f OAS1_0001_MR1_lobulos_lh -b OAS1_0001_MR1 lh Which commands (sintaxis) must I use to compute the white matter volume per each lobe ?... I tested the mri_aparc2aseg and mri_segstats commans with different options, but I couldn't get the volume that I need... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] tip and tricks with patient with one big ventricle...
Hi Nick: Ok... Tomorrow Sunday I will download and begin to test it... And which other new features has version 5.3.0 over 5.2.0 ?... Sincerely, Gonzalo Rojas Costa On Fri, May 3, 2013 at 5:46 PM, Nick Schmansky wrote: > this link is here: > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/ > > the centos6_x86_64 build is there now. the others will appear as they > finish their builds, which can take quite a bit of time... so check back > every day or so.... > > n. -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] tip and tricks with patient with one big ventricle...
Hi Bruce: Ok... I am interested in the 5.3 beta version... Sincerely, Gonzalo Rojas Costa On Fri, May 3, 2013 at 8:41 AM, Bruce Fischl wrote: > Hi Gonzalo > > version 5.3 is midway through the QA process. We can give you a beta of it > in the next couple of days if you want > > Bruce > On Thu, 2 May 2013, Gonzalo Rojas Costa wrote: > >> Hi Bruce: >> >> And, where is version 5.3 ?... in the "nightly dev builds" ?... >> >> Sincerely, >> >> >> Gonzalo Rojas Costa >> >> On Thu, May 2, 2013 at 9:29 PM, Bruce Fischl >> wrote: >>> >>> Hi Gonzalo >>> Try it with 5.3, or upload and I can r. It for you >>> Bruce >>> >>> >>> >>> On May 2, 2013, at 2:16 PM, Gonzalo Rojas Costa >>> wrote: >>> >>>> Hi Bruce: >>>> >>>> I tested 4.5 and 5.1 versions... with the first I processed >>>> complete, and with 5.1 only autorecon1 section... >>>> >>>> Sincerely, >>>> >>>> >>>> Gonzalo Rojas Costa >>>> >>>> >>>> On Thu, May 2, 2013 at 1:31 PM, Bruce Fischl >>>> wrote: >>>>> >>>>> what version are you running? The newer ones are *much* better at this >>>>> Bruce >>>>> >>>>> On Thu, 2 May 2013, Gonzalo Rojas Costa wrote: >>>>> >>>>>> Hi: >>>>>> >>>>>> I has the MPRAGE of a patient with one big ventricle, and the other >>>>>> has normal shape and size... Any tip and tricks to process it ?... >>>>>> Because freesurfer fails from the beggining of the process (VERY BAD >>>>>> talairach registration)... I test -bigventricle option of recon-all, >>>>>> but I got the same problems... >>>>>> >>>>>> Sincerely, >>>>>> >>>>>> -- >>>>>> Gonzalo Rojas Costa >>>>>> Laboratory for Advanced Medical Image Processing >>>>>> Department of Radiology >>>>>> Clínica las Condes >>>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>>>> Tel: 56-2-2105170 >>>>>> Cel: 56-9-97771785 >>>>>> www.clc.cl >>>>>> >>>>>> ___ >>>>>> 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. >>>> >>>> >>>> >>>> >>>> -- >>>> Gonzalo Rojas Costa >>>> Laboratory for Advanced Medical Image Processing >>>> Department of Radiology >>>> Clínica las Condes >>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>> Tel: 56-2-2105170 >>>> Cel: 56-9-97771785 >>>> www.clc.cl >>>> >>>> >> >> >> > -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tip and tricks with patient with one big ventricle...
Hi Bruce: And, where is version 5.3 ?... in the "nightly dev builds" ?... Sincerely, Gonzalo Rojas Costa On Thu, May 2, 2013 at 9:29 PM, Bruce Fischl wrote: > Hi Gonzalo > Try it with 5.3, or upload and I can r. It for you > Bruce > > > > On May 2, 2013, at 2:16 PM, Gonzalo Rojas Costa > wrote: > >> Hi Bruce: >> >> I tested 4.5 and 5.1 versions... with the first I processed >> complete, and with 5.1 only autorecon1 section... >> >> Sincerely, >> >> >> Gonzalo Rojas Costa >> >> >> On Thu, May 2, 2013 at 1:31 PM, Bruce Fischl >> wrote: >>> what version are you running? The newer ones are *much* better at this >>> Bruce >>> >>> On Thu, 2 May 2013, Gonzalo Rojas Costa wrote: >>> >>>> Hi: >>>> >>>> I has the MPRAGE of a patient with one big ventricle, and the other >>>> has normal shape and size... Any tip and tricks to process it ?... >>>> Because freesurfer fails from the beggining of the process (VERY BAD >>>> talairach registration)... I test -bigventricle option of recon-all, >>>> but I got the same problems... >>>> >>>> Sincerely, >>>> >>>> -- >>>> Gonzalo Rojas Costa >>>> Laboratory for Advanced Medical Image Processing >>>> Department of Radiology >>>> Clínica las Condes >>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>> Tel: 56-2-2105170 >>>> Cel: 56-9-97771785 >>>> www.clc.cl >>>> >>>> ___ >>>> 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. >> >> >> >> -- >> Gonzalo Rojas Costa >> Laboratory for Advanced Medical Image Processing >> Department of Radiology >> Clínica las Condes >> Lo Fontecilla 441, Las Condes, Santiago, Chile. >> Tel: 56-2-2105170 >> Cel: 56-9-97771785 >> www.clc.cl >> >> -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tip and tricks with patient with one big ventricle...
Hi Bruce: I tested 4.5 and 5.1 versions... with the first I processed complete, and with 5.1 only autorecon1 section... Sincerely, Gonzalo Rojas Costa On Thu, May 2, 2013 at 1:31 PM, Bruce Fischl wrote: > what version are you running? The newer ones are *much* better at this > Bruce > > On Thu, 2 May 2013, Gonzalo Rojas Costa wrote: > >> Hi: >> >> I has the MPRAGE of a patient with one big ventricle, and the other >> has normal shape and size... Any tip and tricks to process it ?... >> Because freesurfer fails from the beggining of the process (VERY BAD >> talairach registration)... I test -bigventricle option of recon-all, >> but I got the same problems... >> >> Sincerely, >> >> -- >> Gonzalo Rojas Costa >> Laboratory for Advanced Medical Image Processing >> Department of Radiology >> Clínica las Condes >> Lo Fontecilla 441, Las Condes, Santiago, Chile. >> Tel: 56-2-2105170 >> Cel: 56-9-97771785 >> www.clc.cl >> >> ___ >> 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. -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tip and tricks with patient with one big ventricle...
Hi: I has the MPRAGE of a patient with one big ventricle, and the other has normal shape and size... Any tip and tricks to process it ?... Because freesurfer fails from the beggining of the process (VERY BAD talairach registration)... I test -bigventricle option of recon-all, but I got the same problems... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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 5.1 vs 5.2
Hi: How can install version 5.2 in a computer without uninstalling version 5.1 ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] GM and WM volume for each lobe...
Hi: I need to compute the GM and WM volume for each lobe... I know that for GM, I must use: mri_annotation2label --subject bert --hemi rh --lobesStrict lobesfile mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.lobesfile.stats -b -a ../label/lh.lobesfile.annot bert lh white And, for WM I know that I must use the commands: mri_aparc2aseg and mri_segstats, but I don't know the options of each command that I must use... Could you please send me the complete commands for WM?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] default lateral extent corpus callosum
Hi: What is the default thickness of the corpus callosum?... 5 mm ?... 2 mm for each side from midline ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] white/gray surface and volumetric segmentation (aseg) difference...
Hi: With some mprage images, I got differences in the volumetric segmentation (aseg) of the cortex and the white/gray surface... Why ?... I know that both methods are totally different... In the aseg I got some bad segmentation of the cortex, but it in the white/gray surface I got very better results... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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 error...
Hi Anastasia: And, which options do you think I must use with bedpostx ?... The default ?... Sincerely, Gonzalo Rojas Costa On Mon, Jul 30, 2012 at 5:36 PM, Anastasia Yendiki wrote: > > Hi Gonzalo - This has come up a few times recently. Please see here: > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23064.html > > Hope this helps, > a.y -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] tracula error...
Hi: I ran "trac-all -prep -c dmrirc" and it finished ok... Then, when I tried to run the command "trac-all -bedp -c dmrirc", I got the error: ln -sf /usr/local/freesurfer/subjects/bmvf_23_7_2012/dlabel/diff/anat_brain_mask.bbr.nii.gz /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri/nodif_brain_mask.nii.gz ln -sf /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri/dwi.nii.gz /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri/data.nii.gz WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_seychelles /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri subjectdir is /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri Making bedpostx directory structure Queuing preprocessing stages [: 223: NONE: unexpected operator [: 314: NONE: unexpected operator [: 327: xbedpostx_pre: unexpected operator [: 486: x: unexpected operator [: 486: -le: argument expected Queuing parallel processing stage [: 223: NONE: unexpected operator [: 327: xbedpostx: unexpected operator [: 486: x27: unexpected operator 0 slices processed Queuing post processing stage [: 223: NONE: unexpected operator [: 314: NONE: unexpected operator [: 327: xbedpostx_post: unexpected operator [: 486: x: unexpected operator [: 486: -le: argument expected That problem occurr because my PC is not a parallelized environment?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] tracula RAM memory ?...
Hi: How much memory needs tracula to process a DTI study ?... Because my PC (Ubuntu Linux, 4GB RAM) exit because it can't allocate memory in trac-preproc... There exist any tip & trick in such a case?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] tracula processing time ?...
Hi: How much time (aprox) take each step of tracula processing ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] pial mesh decimation...
Hi: How can I do a decimation to 1 polygons aprox to the pial surface ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] Corpus callosum aseg division...
Hi: Any reference about how freesurfer divides the corpus callosum in CC_Posterior, CC_Mid_Posterior, CC_Central, CC_Mid_Anterior, CC_Anterior ?... Sincerely, Gonzalo Rojas Costa ___ 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] mri_cc and CC thickness option...
Hi: For example, if I execute the mri_cc command with "-t 2", mri_cc shows me "setting callosum thickness to 5 mm"... Why ?... What exactly specify the -t option ?... Sincerely, Gonzalo Rojas Costa ___ 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] WM hypointensities included in left-cerebral (right-cerebral) white matter volume ?...
Hi: In aseg.stats the WM hypointensities is included in left-cerebral (right-cerebral) white matter volume ?... Sincerely, Gonzalo Rojas Costa ___ 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] cortical thickness values in a specified gyrus...
Hi: In rh.aparc.a2009s.stats file, appears the average cortical thickness (ThickAvg) value for frontal middle gyrus (G_front_middle): how can I get the values of the cortical thickness in that gyrus (for example), not the average value ?... Sincerely, Gonzalo Rojas Costa ___ 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] cuda error...
Hi: I installed CUDA 4 in a Ubuntu 10.10 based workstation... I tried to process a volume, but I got the following error: "writing output transformation to transforms/talairach_with_skull.lta... CUDA Error in file 'gcasgpu.cu' on line 159 : unspecified driver error. registration took 15 minutes and 1 seconds. Abort"... How can I correct it ?... Sincerely Gonzalo Rojas Costa ___ 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] paper related to subcortical volume in children...
Hi: There exist any paper related to the subcortical volume in children (below 15 years old)?... any image database ?... Sincerely, Gonzalo Rojas Costa ___ 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] volume of different lobes of the brain....
Hi Douglas: The solution that you sent me runs only in freesurfer 5... Do you have ay solution for freesurfer 4.5.0 to compute GM+WM volume for each lobule ?... Sincerely, Gonzalo Rojas Costa On Mon, Sep 26, 2011 at 11:01 AM, Douglas N Greve wrote: > You can run mri_annotation2label with --lobesStrict to get a lobe > annotation. If that definition of "lobes" is good for you, then you can run > mris_anatomical_stats to get the volume for each lobe. > doug ___ 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] volume of different lobes of the brain....
Hi: How can I get the volume of the different lobes of the brain (occipital, parietal, temporal, etc) ?... White matter and gray matter?... Labels ?... Sincerely, Gonzalo Rojas Costa ___ 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] tkmedit bus error
Hi Carolina: Is it possible, but in my case when the hard disk is full at the moment of the processing, I got a fatal error from recon-all command... Sincerely, Gonzalo Rojas Costa El 19-09-2011 9:53, Carolina Valencia escribió: > Thanks for the answers. > I think the problem was the hard disk space, I can open it now in the > views (tksurfer, tkmedit) > > Best regards, > > Carolina ___ 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] tkmedit bus error
Hi Carolina: And did you tested the tksurfer command ?... for example: tksurfer CORBIC_vol01 rh pial Sincerely, Gonzalo Rojas Costa Department of Radiology Clinica Las Condes Santiago Chile > Message: 4 > Date: Sun, 18 Sep 2011 10:25:26 -0400 (EDT) > From: Bruce Fischl > Subject: Re: [Freesurfer] tkmedit bus error > To: Carolina Valencia > Cc: Freesurfer Mailing List > > Hi Carolina, > > does this happen every time? Can you run freeview on the volumes and see > if it can display them properly? > > cheers > Bruce > On Thu, 15 Sep 2011, Carolina Valencia > wrote: > >> Hi FSusers >> >> I run recon-all in a patient without problems, but when I tried to view it >> in tkmedit, an error pops up. >> >> I appreciate your help! >> >> Best regards, >> Carolina >> >> recon-all -s CORBIC_vol01 finished without error at Tue Sep 13 12:42:43 COT >> 2011 >> done >> cvalencia-Precision-WorkStation-T3400:~> tkmedit CORBIC_vol01 brainmask.mgz >> -aux T1.mgz -surfs -segmentation aseg.mgz >> $FREESURFER_HOME/FreeSurferColorLUT.txt >> Bus error >> cvalencia-Precision-WorkStation-T3400:~> tkmedit CORBIC_vol01 brainmask.mgz >> -aux T1.mgz -surfs -segmentation aseg.mgz >> $FREESURFER_HOME/FreeSurferColorLUT.txt >> Bus error ___ 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] optimal sequence in a 1.5 T MR OPTIMA 450w GE MRI equipment...
Hi: Which is the optimal parameters for a morphometric sequence in a 1.5 T MR OPTIMA 450w GE MRI equipment ?... Sincerely, Gonzalo Rojas Costa ___ 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] processing OASIS database using freesurfer 5
Hi: I need to reprocess some images of the OASIS database using freesurfer 5... Should I use only the command "recon-all -s OAS1_0074_MR1 -all", or I must add the option "-expert expert.opts" ?... In the first case freesurfer automatically use thresholds specified in expert.opts ?... Sincerely, Gonzalo Rojas Costa ___ 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] xopts script...
Hi: In the web page "FSTutorial/TroubleshootingData - Free Surfer Wiki" appears "Try using an xopts script first to change the intensity thresholds being used"... What is a xopts script ?... How can I use a xopts script to change the intensity thresholds ?... Sincerely, Gonzalo Rojas Costa ___ 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] WM and ASEG edition... recon-all continue command...
Hi Bruce: I ran with -make all, and I get good results... It seems that freesurfer uses the wm.mgz and aseg.mgz editions that I did... Sincerely, Gonzalo Rojas Costa El 27-07-2011 11:48, Bruce Fischl escribió: > Hi Gonzalo, > > Nick can correct me if I'm wrong, but the intent of -make all is to > detect which steps need to be rerun based on file timestamps. All edits > should also be detected and kept, so it should do the right thing (right > Nick?) > > cheers > Bruce ___ 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] WM and ASEG edition... recon-all continue command...
Hi Bruce: Maybe I didn't explain clearly my question... I did a complete processing of a patient, then I must edit wm.mgz and aseg.mgz because I found some segmentation errors... Which recon-all command must I run to reprocess the study to use the edited files (wm.mgz and aseg.mgz) ?... Sincerely, Gonzalo Rojas Costa El 25-07-2011 18:51, Bruce Fischl escribió: > -make all should work. > > cheers > Bruce > On Mon, 25 Jul 2011, Gonzalo Rojas Costa wrote: > >> Hi >> >> I editted the wm.mgz and aseg.mgz files... Which recon-all command >> must I use to continue the processing ?... >> >> Sincerely, >> >> >> Gonzalo Rojas Costa >> ___ >> 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
